From: Takeru KAMEDA (kamedapon_at_hiroshima-u.ac.jp)
Date: Wed Nov 27 2019 - 00:19:06 CST
Dear Giacomo.
Thank you for your kind reply, and sorry for the late response.
Almostly, I was able to perform ABF well because your attached URL included familiar information.
I will try more.
Thanks.
Best wishes,
Takeru Kameda
PhD Student, Hiroshima University, Japan
________________________________________
差出人: Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
送信日時: 2019年11月7日 4:32
宛先: Takeru KAMEDA
CC: NAMD list
件名: Re: namd-l: Multi canonical ensemble method
Hello Takeru, the dependency error is due to trying to measure a total force for a variable type that doesn't have it implemented. Below is the updated link, which unlike the one you copied earlier, should remain the same in future versions (and thus be useful in searches for this message):
You can still use ABF on an extended-Lagrangian variable, but you probably need to get rid of outputTotalForce. Does that make solve the problem?
The second message about sockets is bogus, sorry. For a while (but not any longer) Colvars has been sharing the error code flag with other functions in NAMD, but it wasn't always set consistently and the numeric code sometimes referred to something completely unrelated, like that. In general, the Colvars module will always print all errors originating there first, and the last "FATAL ERROR" message from the main NAMD function simply refers to that, but does not add any further information.
Giacomo
On Wed, Nov 6, 2019 at 4:58 AM Takeru KAMEDA <kamedapon_at_hiroshima-u.ac.jp<mailto:kamedapon_at_hiroshima-u.ac.jp>> wrote:
Thank you for your kind reply.
And, I will take care to keep the list in CC.
I changed parentheses to curly braces as :
axis {1, 0, 0} → axis (1, 0, 0)
Then, following error message were output :
Excerpt below
""""""""
Are there 2 problems ?
In previous exchange for others, I obtained following manual page
http://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#x1-530005.3.3 But, I cloudn't resolve above problem
Thanks.
Best wishes,
________________________________________
Hello Takeru, please keep the list in CC.
Your error is due to using curly braces instead of parentheses.
Giacomo
On Mon, Nov 4, 2019 at 9:39 PM Takeru KAMEDA <kamedapon_at_hiroshima-u.ac.jp<mailto:kamedapon_at_hiroshima-u.ac.jp><mailto:kamedapon_at_hiroshima-u.ac.jp<mailto:kamedapon_at_hiroshima-u.ac.jp>>> wrote:
Thank you for your kind reply.
I tried ABF as you said using attached files.
However, I obtained attached log file (run.log).
Are there any missing configurauin ?
Thanks
Best wishes,
________________________________________
Hello Takeru, it looks like you already found the documentation, try to double-check that your configuration is consistent. See here an example:
If it is consistent with the doc, do you mind pasting it in the email or attaching it?
Giacomo
On Wed, Oct 30, 2019 at 1:28 AM Takeru KAMEDA <kamedapon_at_hiroshima-u.ac.jp<mailto:kamedapon_at_hiroshima-u.ac.jp><mailto:kamedapon_at_hiroshima-u.ac.jp<mailto:kamedapon_at_hiroshima-u.ac.jp>><mailto:kamedapon_at_hiroshima-u.ac.jp<mailto:kamedapon_at_hiroshima-u.ac.jp><mailto:kamedapon_at_hiroshima-u.ac.jp<mailto:kamedapon_at_hiroshima-u.ac.jp>>>> wrote:
Thank you for your advice.
I changed the method orientation to spinAngle.
Now I'm trying such method.
In this case, I think I must set the axis of rotation and center of roration.
Do you know how to set such axis and center.
Best wishes,
________________________________________
Dear Takeru,
this "failed dependency" message indicates that ABF only supports scalar variables. A multidimensional ABF calculation can be done with several scalar variables, not a single vector one.
In this case, the orientation variable is 4-dimensional, which is probably too much for ABF anyway. I recommend reducing your sampling space to 1, 2 or 3 scalar quantities.
Best wishes,
On Mon, 30 Sep 2019 at 04:23, Takeru KAMEDA <kamedapon_at_hiroshima-u.ac.jp<mailto:kamedapon_at_hiroshima-u.ac.jp><mailto:kamedapon_at_hiroshima-u.ac.jp<mailto:kamedapon_at_hiroshima-u.ac.jp>><mailto:kamedapon_at_hiroshima-u.ac.jp<mailto:kamedapon_at_hiroshima-u.ac.jp><mailto:kamedapon_at_hiroshima-u.ac.jp<mailto:kamedapon_at_hiroshima-u.ac.jp>>><mailto:kamedapon_at_hiroshima-u.ac.jp<mailto:kamedapon_at_hiroshima-u.ac.jp><mailto:kamedapon_at_hiroshima-u.ac.jp<mailto:kamedapon_at_hiroshima-u.ac.jp>><mailto:kamedapon_at_hiroshima-u.ac.jp<mailto:kamedapon_at_hiroshima-u.ac.jp><mailto:kamedapon_at_hiroshima-u.ac.jp<mailto:kamedapon_at_hiroshima-u.ac.jp>>>>> wrote:
Hi. I am trying multi-canonical ensemble method using NAMD2.13.
I wrote colvar file as follows:
colvarsTrajFrequency 5000
colvar {
outputValue on
orientation {
abf {
Then, we execute simulation, following error was output:
colvars: ----------------------------------------------------------------------
Any parts of configulation file was wrong?
Best wishes,
This archive was generated by hypermail 2.1.6
: Tue Dec 31 2019 - 23:21:02 CST
https://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#sec:cvc_sys_forces
Dear Giacomo.
colvars: ----------------------------------------------------------------------
colvars: Collective variables initialized, 1 in total.
colvars: ----------------------------------------------------------------------
colvars: Initializing a new "abf" instance.
colvars: # name = "abf1" [default]
colvars: # colvars = { theta }
colvars: # outputEnergy = off [default]
colvars: # timeStepFactor = 1 [default]
colvars: # applyBias = on [default]
colvars: # updateBias = on [default]
colvars: # hideJacobian = on
colvars: Jacobian (geometric) forces will be handled internally.
colvars: # fullSamples = 200
colvars: # inputPrefix = [default]
colvars: # outputFreq = 50000 [default]
colvars: # historyFreq = 0 [default]
colvars: # shared = off [default]
colvars: "total force" in colvar theta requires one of the following features, none of which can be enabled:
colvars: -----------------------------------------
colvars: 1. extended Lagrangian
colvars: User-controlled feature "extended Lagrangian" may not be enabled as a dependency in colvar theta.
colvars: 2. total force calculation
colvars: Dynamic feature unavailable: "Jacobian derivative" in cvc tilt0001.
colvars: ...required by "Jacobian derivative" in colvar theta
colvars: ...required by "total force calculation" in colvar theta
colvars: -----------------------------------------
colvars: ...required by "obtain total force" in bias abf1
colvars: Error: Failed dependency in bias abf1.
FATAL ERROR: Error in the collective variables module: Socket operation on non-socket
""""""""
Takeru Kameda
PhD Student, Hiroshima University, Japan
差出人: Giacomo Fiorin <giacomo.fiorin_at_gmail.com<mailto:giacomo.fiorin_at_gmail.com>>
送信日時: 2019年11月5日 22:18
宛先: Takeru KAMEDA
CC: NAMD list
件名: Re: namd-l: Multi canonical ensemble method
Dear Giacomo
Takeru Kameda
PhD Student, Hiroshima University, Japan
差出人: Giacomo Fiorin <giacomo.fiorin_at_gmail.com<mailto:giacomo.fiorin_at_gmail.com><mailto:giacomo.fiorin_at_gmail.com<mailto:giacomo.fiorin_at_gmail.com>>>
送信日時: 2019年10月30日 23:22
宛先: Takeru KAMEDA
CC: Jérôme Hénin; namd-l
件名: Re: namd-l: Multi canonical ensemble method
https://raw.githubusercontent.com/Colvars/colvars/master/tests/spinangle.in
868d8e12640d3750%7C1%7C0%7C637086658022508253&sdata=98HCdVmsdAUR3vUK0IOt9ZHlBj7CmXFGJQAPHywsrys%3D&reserved=0>><https://jpn01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fraw.githubusercontent.com%2FColvars%2Fcolvars%2Fmaster%2Ftests%2Fspinangle.in&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7Cdc8ab578dcfd4144be5308d75d44c110%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637080422187028882&sdata=uDrPerxN1ceCjrQhZ4yfQ9Qpp3xln2AQwhnE4Cs%2B5ak%3D&reserved=0<https://jpn01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fraw.githubusercontent.com%2FColvars%2Fcolvars%2Fmaster%2Ftests%2Fspinangle.in&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7C52f0f5f44b8d47b29ea508d762f0a53e%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637086658022518247&sdata=GHiXM3FuX9w6aqYOOtG61P6xDlUziXOKR9c8be%2Benvg%3D&reserved=0><https://jpn01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fraw.githubusercontent.com%2FColvars%2Fcolvars%2Fmaster%2Ftests%2Fspinangle.in&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7C99bf!
f67013fc
4
0e50bd008d761f2e924%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637085568234920878&sdata=soTnsL1ev1023QcQwGrqktuaU1TLk92cFx00B3PPUwA%3D&reserved=0<https://jpn01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fraw.githubusercontent.com%2FColvars%2Fcolvars%2Fmaster%2Ftests%2Fspinangle.in&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7C52f0f5f44b8d47b29ea508d762f0a53e%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637086658022518247&sdata=GHiXM3FuX9w6aqYOOtG61P6xDlUziXOKR9c8be%2Benvg%3D&reserved=0>>>
Hi Jerome.
And, sorry for the late reply.
https://www.ks.uiuc.edu/Research/namd/2.13/ug/node55.html#24897
58022528241&sdata=jXqIBRbJC%2FJnt%2BM6KlD3viB24ltJyhtJBhRDlrOiMh0%3D&reserved=0>><https://jpn01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ks.uiuc.edu%2FResearch%2Fnamd%2F2.13%2Fug%2Fnode55.html%2324897&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7Cdc8ab578dcfd4144be5308d75d44c110%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637080422187028882&sdata=XY27Nbbf20n3dSyNa%2BJOc7key7RYeJHD3602iGzuaMU%3D&reserved=0<https://jpn01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ks.uiuc.edu%2FResearch%2Fnamd%2F2.13%2Fug%2Fnode55.html%2324897&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7C52f0f5f44b8d47b29ea508d762f0a53e%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637086658022538233&sdata=QJqGcYXh%2FudnCo0Y13JFZ8O4Nb1L%2FK8aWlRhHbAOWZU%3D&reserved=0><https://jpn01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ks.uiuc.edu%2FResearch%2Fnamd%2F2.13%2Fug%2Fnode55.html%2324897&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7C99bff67013fc40e50bd008d761f2e924%7Cc40454ddb2634926868d8e12640!
d3750%7C
1
%7C0%7C637085568234930867&sdata=D88d4MWTzKi%2Fw2Atyjk5rNhWkB5%2BqEQxH7kx2M3a2pc%3D&reserved=0<https://jpn01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ks.uiuc.edu%2FResearch%2Fnamd%2F2.13%2Fug%2Fnode55.html%2324897&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7C52f0f5f44b8d47b29ea508d762f0a53e%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637086658022538233&sdata=QJqGcYXh%2FudnCo0Y13JFZ8O4Nb1L%2FK8aWlRhHbAOWZU%3D&reserved=0>>>
However, I can not set "axis" part in "List of keywords" of spinAngle.
Takeru Kameda
PhD Student, Hiroshima University, Japan
差出人: Jérôme Hénin <jerome.henin_at_ibpc.fr<mailto:jerome.henin_at_ibpc.fr><mailto:jerome.henin_at_ibpc.fr<mailto:jerome.henin_at_ibpc.fr>><mailto:jerome.henin_at_ibpc.fr<mailto:jerome.henin_at_ibpc.fr><mailto:jerome.henin_at_ibpc.fr<mailto:jerome.henin_at_ibpc.fr>>>>
送信日時: 2019年9月30日 20:49
宛先: Takeru KAMEDA
CC: namd-l
件名: Re: namd-l: Multi canonical ensemble method
Jerome
Dear all.
colvarsRestartFrequency 50000
name theta
#outputVelocity on
#outputEnergy on
#outputSystemForce on
#outputAppliedForce on
atoms { atomnumbers {
13754 13755 13756 13757 13758 13761 13783 13785 19290 19291 19292 19293 19294 19297 19319 19321
}}
refPositionsFile ./colvar.pdb
refPositionsCol O
}
}
colvars theta
fullSamples 200
hideJacobian
}
colvars: Initializing the collective variables module, version 2018-10-16.
colvars: Please cite Fiorin et al, Mol Phys 2013:
colvars: http://dx.doi.org/10.1080/00268976.2013.813594
d=0>><https://jpn01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdx.doi.org%2F10.1080%2F00268976.2013.813594&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7Cdc8ab578dcfd4144be5308d75d44c110%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637080422187028882&sdata=XmoQr1L3vQpRC78cVcnJTBoIOdxDMuKsgqMiFa87KuI%3D&reserved=0<https://jpn01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdx.doi.org%2F10.1080%2F00268976.2013.813594&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7C52f0f5f44b8d47b29ea508d762f0a53e%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637086658022558224&sdata=R%2FRZdkcPMjCjkKx9tQJnndWKREENfZrCVD69iiTUlkM%3D&reserved=0><https://jpn01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdx.doi.org%2F10.1080%2F00268976.2013.813594&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7C99bff67013fc40e50bd008d761f2e924%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637085568234940862&sdata=RMPbHAIKwMTNNhrqaCMzz%2B8C9D4ujwC4SnBH%2Bv%2FVUB8%3D&reserved=0<https://jpn01.safelinks.protection.outlook.com/?ur!
l=http%3
A
%2F%2Fdx.doi.org%2F10.1080%2F00268976.2013.813594&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7C52f0f5f44b8d47b29ea508d762f0a53e%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637086658022558224&sdata=R%2FRZdkcPMjCjkKx9tQJnndWKREENfZrCVD69iiTUlkM%3D&reserved=0>>><https://jpn01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdx.doi.org%2F10.1080%2F00268976.2013.813594&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7Cf27084172a614d43e33e08d7459c5a6e%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637054410151677447&sdata=rWfUPJdN2KjCG78tilAQa%2B4fGUzllIGohj%2FsQTT8PBo%3D&reserved=0<https://jpn01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdx.doi.org%2F10.1080%2F00268976.2013.813594&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7C52f0f5f44b8d47b29ea508d762f0a53e%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637086658022568216&sdata=zENT26PgZcLPVSnKp9DRxxqqHC%2B0q2R100qSwBwBnVU%3D&reserved=0><https://jpn01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdx.doi.org%2F10.1080%2F00268976.2013.813594&data=02%7C
01%7Ckamedapon%40hiroshima-u.ac.jp%7C99bff67013fc40e50bd008d761f2e924%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637085568234950855&sdata=zN%2F%2FfArDJUCDBwN6t5aVPSvabYEQgLwKtrRBtHEEMTE%3D&reserved=0<https://jpn01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdx.doi.org%2F10.1080%2F00268976.2013.813594&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7C52f0f5f44b8d47b29ea508d762f0a53e%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637086658022568216&sdata=zENT26PgZcLPVSnKp9DRxxqqHC%2B0q2R100qSwBwBnVU%3D&reserved=0>><https://jpn01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdx.doi.org%2F10.1080%2F00268976.2013.813594&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7Cdc8ab578dcfd4144be5308d75d44c110%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637080422187038878&sdata=2pBfCDjzEeNgVGzI4Vvys75ihIU%2B0UmxyZSWbVho7qk%3D&reserved=0<https://jpn01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdx.doi.org%2F10.1080%2F00268976.2013.813594&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7C52f0f5f44b8d47b29e!
a508d762
f
0a53e%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637086658022578210&sdata=UMg6Vo2Y9FnErQVsDhDYw1WwccqCH6UHpGsKvossstc%3D&reserved=0><https://jpn01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdx.doi.org%2F10.1080%2F00268976.2013.813594&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7C99bff67013fc40e50bd008d761f2e924%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637085568234950855&sdata=zN%2F%2FfArDJUCDBwN6t5aVPSvabYEQgLwKtrRBtHEEMTE%3D&reserved=0<https://jpn01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdx.doi.org%2F10.1080%2F00268976.2013.813594&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7C52f0f5f44b8d47b29ea508d762f0a53e%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637086658022578210&sdata=UMg6Vo2Y9FnErQVsDhDYw1WwccqCH6UHpGsKvossstc%3D&reserved=0>>>>
colvars: in any publication based on this calculation.
colvars: SMP parallelism is available.
colvars: Using NAMD interface, version 2018-08-29.
colvars: ----------------------------------------------------------------------
colvars: Reading new configuration from file "colvar.in<https://jpn01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fcolvar.in&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7C52f0f5f44b8d47b29ea508d762f0a53e%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637086658022588215&sdata=X5IHCcu3yEOAWlUteEI2P4rD%2FlrjIW5tZLWwqlDDMdY%3D&reserved=0><https://jpn01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fcolvar.in&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7C99bff67013fc40e50bd008d761f2e924%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637085568234960850&sdata=1R0sCKeduqJvUe%2F1IiZY50O%2Bo7yfK2BobWyC7g374iU%3D&reserved=0<https://jpn01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fcolvar.in&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7C52f0f5f44b8d47b29ea508d762f0a53e%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637086658022588215&sdata=X5IHCcu3yEOAWlUteEI2P4rD%2FlrjIW5tZLWwqlDDMdY%3D&reserved=0>><https://jpn01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fcolvar.in&data=02%7C01%7Ckamedapon%40hiros
hima-u.ac.jp%7Cdc8ab578dcfd4144be5308d75d44c110%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637080422187038878&sdata=leM0XqO1VigPxWB0GKsLZLs4xByxyzWptn12gBG%2FhSo%3D&reserved=0<https://jpn01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fcolvar.in&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7C52f0f5f44b8d47b29ea508d762f0a53e%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637086658022598202&sdata=T09oOzTPoLpB7gLXDUUl1Nb8E0NtInhErxWimKDUEOM%3D&reserved=0><https://jpn01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fcolvar.in&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7C99bff67013fc40e50bd008d761f2e924%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637085568234960850&sdata=1R0sCKeduqJvUe%2F1IiZY50O%2Bo7yfK2BobWyC7g374iU%3D&reserved=0<https://jpn01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fcolvar.in&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7C52f0f5f44b8d47b29ea508d762f0a53e%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637086658022598202&sdata=T09oOzTPoLpB7gLXDUUl1Nb8E0NtInhErxWimKDUEO!
M%3D&res
e
rved=0>>><https://jpn01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fcolvar.in&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7Cf27084172a614d43e33e08d7459c5a6e%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637054410151677447&sdata=LJa3HRG3d3Dm8g91Di2YvRf5owBoU%2F8jCjT3Mzk1680%3D&reserved=0<https://jpn01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fcolvar.in&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7C52f0f5f44b8d47b29ea508d762f0a53e%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637086658022608194&sdata=iCMRUub3jVZOk2B364Iz%2Flh2XemqYQebbRPY5ITIajA%3D&reserved=0><https://jpn01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fcolvar.in&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7C99bff67013fc40e50bd008d761f2e924%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637085568234970844&sdata=3d1h%2FiNeL9Hzk3KElhniiMNQYqvKGRxT%2FJtOsUW7XW4%3D&reserved=0<https://jpn01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fcolvar.in&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7C52f0f5f44b8d47b29ea508d762f0a53e%
7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637086658022608194&sdata=iCMRUub3jVZOk2B364Iz%2Flh2XemqYQebbRPY5ITIajA%3D&reserved=0>><https://jpn01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fcolvar.in&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7Cdc8ab578dcfd4144be5308d75d44c110%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637080422187048867&sdata=j6GeGCLQRPbtIOYvjRC5J9rErGcUyK9QCcuOqG7WPH4%3D&reserved=0<https://jpn01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fcolvar.in&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7C52f0f5f44b8d47b29ea508d762f0a53e%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637086658022618193&sdata=HlqVPbNtvP%2B4KBN8ZOBF52PH7Ky1sKaRABEzNpLlTTA%3D&reserved=0><https://jpn01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fcolvar.in&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7C99bff67013fc40e50bd008d761f2e924%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637085568234980839&sdata=H7hoGAWkNu2sJdWx63GIshDVUqfK%2B8vkYtWyaWgV2jQ%3D&reserved=0<https://jpn01.safelinks.protec!
tion.out
l
ook.com/?url=http%3A%2F%2Fcolvar.in&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7C52f0f5f44b8d47b29ea508d762f0a53e%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637086658022618193&sdata=HlqVPbNtvP%2B4KBN8ZOBF52PH7Ky1sKaRABEzNpLlTTA%3D&reserved=0>>>>":
colvars: # smp = on [default]
colvars: # analysis = off [default]
colvars: # colvarsTrajFrequency = 5000
colvars: # colvarsRestartFrequency = 50000
colvars: # scriptedColvarForces = off [default]
colvars: # scriptingAfterBiases = off [default]
colvars: ----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = "theta"
colvars: Initializing a new "orientation" component.
colvars: # name = "" [default]
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # period = 0 [default]
colvars: # wrapAround = 0 [default]
colvars: # forceNoPBC = off [default]
colvars: # scalable = on [default]
colvars: Initializing atom group "atoms".
colvars: # name = "" [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # atomsOfGroup = "" [default]
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # enableFitGradients = on [default]
colvars: # printAtomIDs = off [default]
colvars: Atom group "atoms" defined, 16 atoms initialized: total mass = 195.991, total charge = -1.86.
colvars: # refPositions = [default]
colvars: # refPositionsFile = "./colvar.pdb"
colvars: # refPositionsCol = "O"
colvars: # refPositionsColValue = 0 [default]
Info: Found 351 unique exclusion lists needing 1152 bytes
Info: Found 351 unique exclusion lists needing 1152 bytes
Info: Found 351 unique exclusion lists needing 1152 bytes
Info: Found 351 unique exclusion lists needing 1152 bytes
colvars: Centering the reference coordinates: it is assumed that each atom is the closest periodic image to the center of geometry.
colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default]
colvars: All components initialized.
colvars: # timeStepFactor = 1 [default]
colvars: # width = 1 [default]
colvars: # expandBoundaries = off [default]
colvars: # extendedLagrangian = off [default]
colvars: # outputValue = on
colvars: # outputVelocity = off [default]
colvars: # outputTotalForce = off [default]
colvars: # outputAppliedForce = off [default]
colvars: # subtractAppliedForce = off [default]
colvars: ----------------------------------------------------------------------
colvars: Collective variables initialized, 1 in total.
colvars: ----------------------------------------------------------------------
colvars: Initializing a new "abf" instance.
colvars: # name = "abf1" [default]
colvars: # colvars = { theta }
colvars: # outputEnergy = off [default]
colvars: # timeStepFactor = 1 [default]
colvars: Static feature "scalar" may not be enabled as a dependency in colvar theta.
colvars: ...required by "require scalar variables" in bias abf1
colvars: Error: Failed dependency in bias abf1.
FATAL ERROR: Error in the collective variables module: exiting.
Takeru Kameda
PhD Student, Hiroshima University, Japan
--
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Research collaborator, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU