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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