Re: water box getting deformed

From: Eric H. Lee (ericlee_at_ks.uiuc.edu)
Date: Thu Dec 11 2008 - 07:45:58 CST

Why did you turn off periodic boundary conditions? That explains why
your system dimensions are deforming.

-Eric

On Dec 11, 2008, at 7:06 AM, sunita gupta wrote:

> Hi
> I am simulating a protein around 350 residues. The minimization and
> heating went fine, but after equilibrating the system for 200 ps,
> the shape of the water box gets deformed (somewhat octagonal)...Can
> anyone suggest what might be the reason?. I have commented out the
> cellbasisvector in the configuration file. The rmsd is also shooting
> up during equilibration. Below is the configuration file that I used.
> Any suggestion will be appreciated.
>
> #Minimization and Equilibriation
> set inputname try_heat
> structure pro_wi.psf
> coordinates pro_wi.pdb
> #set temperature 310
> set outputname pro_equi
> bincoordinates $inputname.restart.coor
> binvelocities $inputname.restart.vel
> extendedSystem $inputname.restart.xsc
>
>
> proc get_first_ts { xscfile } {
> set fd [open $xscfile r]
> gets $fd
> gets $fd
> gets $fd line
> set ts [lindex $line 0]
> close $fd
> return $ts
> }
>
> set currenttimestep [get_first_ts $inputname.restart.xsc]
> #set currenttimestep 0
>
> firsttimestep $currenttimestep
>
>
> #Input
> paraTypeCharmm on
> parameters par_all22_prot_cmap.inp
> #temperature $temperature
>
> #Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 12
> switching on
> switchdist 10
> pairlistdist 14
>
> #Integrator Parameters
> timestep 2.0
> rigidBonds all
> nonbondedFreq 2
> fullElectFrequency 4
> stepspercycle 20
>
>
> #Constant Temperature Control
> langevin on
> langevinDamping 5
> langevinTemp 300
> langevinHydrogen no
>
> #periodic boundary conditions
> #cellBasisVector1 110.56 00.00 00.00
> #cellBasisVector2 00.00 129.55 00.00
> #cellBasisVector3 00.00 00.00 213.95
> cellOrigin 55.27 65.18 106.93
> wrapWater on
> wrapAll on
> PME yes
> PMEGridSizeX 120
> PMEGridSizeY 135
> PMEGridSizeZ 225
>
> #Constant Pressure Control
> useGroupPressure yes
> useFlexibleCell yes
> #useConstantArea yes
> langevinPiston on
> langevinPistonTarget 1.01325
> langevinPistonPeriod 200
> langevinPistonDecay 100
> langevinPistonTemp 300
>
> #Output
> OutputName $outputname
> binaryoutput no
> restartfreq 1000
> dcdfreq 1000
> outputEnergies 1000
> outputPressure 1000
> xstFreq 1000
> binaryrestart yes
>
> #Execution Script
> #minimize 3500
> #reinitvels $temperature
>
> run 100000
>
>
>
> Thanks and regards
> --
> SUNITA GUPTA
> Member Research Team
> Lead Invent Technology
> TBIU, IIT Delhi, India
> Email- sunita_at_leadinvent.com
> Ph- +9111 26581524 (Ex-6)

Eric H. Lee
Medical Scholars Program
Theoretical and Computational Biophysics Group, UIUC
ericlee_at_ks.uiuc.edu

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