From: Rabab Toubar (rtoubar_at_yahoo.com)
Date: Wed Apr 29 2009 - 20:59:41 CDT
Hi all,
I was just wondering how would the protein move without the water box when Eric is using "wrapAll"
Rabab
--- On Wed, 4/29/09, Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu> wrote:
From: Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu>
Subject: Re: namd-l: protein shifts out of the water box
To: "Eric Userlist" <eric.userlist_at_gmail.com>
Cc: namd-l_at_ks.uiuc.edu
Date: Wednesday, April 29, 2009, 8:14 PM
On Wed, 2009-04-29 at 16:52 -0700, Eric Userlist wrote:
> Hi
> I am running a md simulation with the following input file. After I
> examine the trajectory, part of the protein is outside the water grid.
> I solvate the protein with 9 angstrom from the edge of the grid.
> Should I use a bigger water box or restrain the protein somehow.
eric,
please consider that you have periodic boundary conditions.
your water has a suspiciously large hole, right? ;)
apart from that, it is probably a good idea to check the
motion of the total center of mass and remove it. this kind
of drift would be leading to having the system being colder
than the kinetic energy idicates. think of an extremely
fast icecube as an extreme example of that...
cheers,
axel.
> Thank you.
>
> Eric
>
> ###### Input Files and Parameters #######
>
> set temperature 310
> set outputname protein_md2
> set restartfreq 500
>
> structure ../common/protein_ionized.psf
> coordinates ../md/protein_md.pdb
> bincoordinates ../md/protein_md.restart.coor
> binvelocities ../md/protein_md.restart.vel
> extendedSystem ../md/protein_md.xsc
>
> ######################
> # Force-Field Parameters
> paratypecharmm on
> parameters ../common/par_all27_prot_lipid.inp
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 9.
> switching on
> switchdist 8.
> pairlistdist 11
>
> # Integrator Parameters
> timestep 1.0 ;# 2fs/step
> rigidBonds all ;# needed for 2fs steps
> rigidTolerance 0.00000001
> margin 2.5
> nonbondedFreq 2
> fullElectFrequency 4
> stepspercycle 20
>
> # Temperature Control
> langevin on
> langevinTemp 310
> langevinDamping 1
> #temperature $temperature
> #reassignFreq 100
> #reassignTemp 25
> #reassignIncr 25
> #reassignHold 300
>
> # Periodic Boundary Conditions
> cellBasisVector1 66.3 0 0
> cellBasisVector2 0 71.5 0
> cellBasisVector3 0 0 78.9
> cellOrigin 23.77 24.54 11.70
> wrapAll on
> wrapNearest on
>
> # PME (for full-system periodic electrostatics)
> PME yes
> PMEGridSizeX 72
> PMEGridSizeY 72
> PMEGridSizeZ 80
>
> # Constant Pressure Control (variable volume)
> useGroupPressure yes
> useFlexibleCell no
> LangevinPiston on
> LangevinPistonTarget 1
> LangevinPistonPeriod 200
> LangevinPistonDecay 500
> LangevinPistonTemp 310
>
> # Output
> outputname $outputname
> outputEnergies 10
> restartfreq $restartfreq
> DCDfreq 500
> binaryoutput no
> binaryrestart yes
> outputTiming 100
>
>
> ########## Extra Parameters ################
>
> # Constraints
> #constraints on
> #consref ../min/protein_min.pdb
> #conskfile ../min/protein_min_constraint.pdb
> #conskcol B
>
> ########## Execution ##############
>
> #minimize 1000
>
> run 10000000
>
>
>
-- ======================================================================= Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot.
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