Re: water box getting deformed

From: Joshua Adelman (jadelman_at_berkeley.edu)
Date: Thu Dec 11 2008 - 11:01:34 CST

Sunita,

If you're restarting from a previous simulation you should be
commenting out the cellbasisvector parameters (or rather it shouldn't
make a difference since the PBC is read from the extended system
file). So I don't think that's the problem.

Also when you say that the RMSD is 'shooting up' what does that mean
exactly. Is your system blowing up and you're seeing wild deformations
of bonds? Or is it getting larger and then settling down after some
finite time (which will depend on the size of your system)?

Also you are using a flexiblecell, for what seems to be just a protein
system, which is not usually recommended.

Josh

On Dec 11, 2008, at 5:45 AM, Eric H. Lee wrote:

> 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
>

------------------------------------------------------------------------------------------------------
Joshua L. Adelman
Biophysics Graduate Group Lab: 510.643.2159
218 Wellman Hall Fax: 510.642.7428
University of California, Berkeley http://nature.berkeley.edu/~jadelman
Berkeley, CA 94720 USA jadelman_at_berkeley.edu
------------------------------------------------------------------------------------------------------

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