From: Hocine El Khaoudi enyoury (hocinee6_at_gmail.com)
Date: Wed Nov 23 2022 - 04:47:30 CST
Dear,
Thank you for your help! It worked.
Best Regards,
Hocine
Le 21 nov. 2022 à 16:04 +0100, Josh Vermaas <vermaasj_at_msu.edu>, a écrit :
> More explicitly, the if statement within the loop doesn't close before opening the else. The lines should look like:
>
> run $freq
> } else {
> useGroupPressure yes ;# needed for rigidBonds
>
> -Josh
>
> On 11/21/22 9:09 AM, Giacomo Fiorin wrote:
> > Please look more carefully, you are missing a closing brace.
> >
> > > On Mon, Nov 21, 2022 at 9:01 AM Hocine El Khaoudi enyoury <hocinee6_at_gmail.com> wrote:
> > > > Dear Giacomo,
> > > >
> > > >
> > > > Yes, I have checked. Is there anyway to set a flag to say from 0-100k increase in NVT, 100-200K NPT , and 200-300K NPT? Im not that expert with tcl scripting.
> > > >
> > > > Best Regards,
> > > >
> > > > Hocine
> > > > El 21 nov 2022, 14:59 +0100, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>, escribió:
> > > > > Have you checked that your opening/closing braces match?
> > > > >
> > > > > > On Mon, Nov 21, 2022 at 6:58 AM Hocine El Khaoudi enyoury <hocinee6_at_gmail.com> wrote:
> > > > > > > Dear all,
> > > > > > >
> > > > > > > I’m trying to perform a gradual heating of my system on the following way: Heat to 100K-NPT-Heat to 200K-NPT-Heat to 300K.
> > > > > > >
> > > > > > > I implemented the following loop on my config file but I get the following message error:
> > > > > > > set freq 1000
> > > > > > > for {set i 0} {$i <= $temperature} {incr i 5} {
> > > > > > > if {( $i != 100 ) || ( $i != 200 )} {
> > > > > > > langevinTemp $i
> > > > > > > reinitvels $i
> > > > > > > run $freq
> > > > > > > else {
> > > > > > > useGroupPressure yes ;# needed for rigidBonds
> > > > > > > useFlexibleCell no
> > > > > > > useConstantArea no
> > > > > > > langevinPiston on
> > > > > > > langevinPistonTarget 1.01325 ;# in bar -> 1 atm
> > > > > > > langevinPistonPeriod 100.0
> > > > > > > langevinPistonDecay 50.0
> > > > > > > langevinPistonTemp $i
> > > > > > > run $freq/10
> > > > > > > }
> > > > > > > }
> > > > > > >
> > > > > > > ERROR
> > > > > > >
> > > > > > > FATAL ERROR: parameter value too long for NAMD config parameter
> > > > > > > while executing
> > > > > > > "else {
> > > > > > > useGroupPressure yes ;# needed for rigidBonds
> > > > > > > useFlexibleCell no
> > > > > > > useConstantArea no
> > > > > > > langevinPiston on
> > > > > > > langevi..."
> > > > > > > ("for" body line 6)
> > > > > > > invoked from within
> > > > > > > "for {set i 0} {$i <= $temperature} {incr i 5} {
> > > > > > > if {( $i != 100 ) || ( $i != 200 )} {
> > > > > > > langevinTemp $i
> > > > > > > reinitvels $i
> > > > > > > run $freq/10
> > > > > > > el..."
> > > > > > >
> > > > > > > Would you have any suggestion or tip?
> > > > > > >
> > > > > > > Thanks in advance!
> > > > > > >
> > > > > > > Hocine
>
> --
> Josh Vermaas
>
> vermaasj_at_msu.edu
> Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
> Michigan State University
> vermaaslab.github.io
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