Re: waterbox changes shape during steered molecular dynamics

From: Mert Gür (gurmert_at_gmail.com)
Date: Sat Jul 03 2010 - 05:58:39 CDT

Dear all,
The interesting part is that if set

fixedAtoms off

and

SMD off

I dont observe any deformation.

Additionally this is the only system I observe this problem.

I would be really great if someone could share their comments
regarding what the problem might be.

Best,
Mert

On Mon, Jun 21, 2010 at 10:13 PM, Mert Gür <gurmert_at_gmail.com> wrote:
> Dear all,
> I am trying to do steered molecular dynamics starting from random
> structures in the trajectory.
> For that reason I am loading the trajectory to VMD and then simply
> save the selected frames as pdb files.
> I am using them as initial structures for SMD.
> Since I cant use restart files anymore, I am setting the temperature
> and the cellBasisvector at the beginning
> The waterbox changes its shape significantly during the simulation. I
> have attached the snapshot.
> I observed such an behaviour only ones when I had forgotten to set the
> periodic boundary conditions and the water
> approached its minimum energy shape which is a sphere.
> Does this make sense to anyone?
> Best,
> Mert
>
>
>
>
>
> ######################################################
> ## INPUT AND OUTPUT FILES                           ##
> ######################################################
>
> structure         ../common/ionized.psf
> coordinates       smdref550.pdb
> set temperature    310
> set outputname     B52
> set restartname    res
>
>
> firsttimestep      0
> # Input
> paraTypeCharmm      on
> parameters          ../common/par_all27_prot_lipid.inp
> temperature         $temperature
>
>
> #############################################################
> ## SIMULATION PARAMETERS                                   ##
> #############################################################
>
>
>
> if {1} {
> cellBasisVector1    116.0140    0.   0.
> cellBasisVector2     0.   70.3120   0.
> cellBasisVector3     0.    0   72.9940
> cellOrigin           11.1565 -2.1352 2.7055
> }
> wrapWater           on
> wrapAll             on
>
>
>
>
> # Force-Field Parameters
> exclude             scaled1-4
> 1-4scaling          1.0
> cutoff              12.
> switching           on
> switchdist          10.
> pairlistdist        13.5
>
>
> # Integrator Parameters
> timestep            1.0
> rigidBonds          none
> nonbondedFreq       1
> fullElectFrequency  1
> stepspercycle       5
>
>
>
>
>
>
> # PME (for full-system periodic electrostatics)
> PME                 yes
> PMEGridSizeX        120
> PMEGridSizeY        72
> PMEGridSizeZ        75
>
>
> # Constant Temperature Control
> langevin            on
> langevinDamping     5
> langevinTemp        $temperature
> langevinHydrogen    on
>
>
>
> #############################################################
> ## EXTRA PARAMETERS                                        ##
> #############################################################
>
> if {1} {
> fixedAtoms          on
> fixedAtomsFile      smdref.pdb
> fixedAtomsCol       B
> }
>
> SMD on
> SMDFile smdref.pdb
> #Spring constant
> SMDk 5
> #Bu sayi 15/timestep olacak
> SMDVel 0.00001
> SMDDir 0.7927 -0.5241 -0.3113
> SMDOutputFreq 10
>
>
>
>
>
> # Output
> outputName          $outputname
> restartName         $restartname
> outputEnergies      500
> outputPressure      500
> restartfreq         10000
> dcdfreq             500
> xstFreq             10000
>
>
> run 2500000
>
>

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