Re: restart from different snap shots

From: Mert Gür (gurmert_at_gmail.com)
Date: Tue Aug 10 2010 - 07:48:32 CDT

Dear Jorgen,
If your are doing an N,V,T simulation, the .xsc files do not
change.The xsc file has the parameters that you are looking for.
If you are doing an N,P,T simulation I do not see any reason why you
should not be able to start from any pdb file.

So for an N,V,T ensemble your conf file should start as

structure The psf file you have generated at the beginning of your MD
coordinates the new pdb file that you got from VMD
extendedSystem Any of your .xsc files

temperature Do not forget to set the temperatures since you do
not have a velocity restart file

So for an N,V,T ensemble your conf file should start as

structure The psf file you have generated at the beginning of your MD
coordinates the new pdb file that you got from VMD
temperature Do not forget to set the temperatures since you do
not have a velocity restart file

(Measure these values again)
cellBasisVector1 100. 0. 0.
cellBasisVector2 0. 100. 0.
cellBasisVector3 0. 0. 100.
cellOrigin 0. 0. 0.

The PME parameters can stay the same for all simulations. Even if you
do an N,P,T simulation volume change won't be that drastic so that you
had to change the PME parameters

I hope that helps you.
Best,
Mert

On Tue, Aug 10, 2010 at 2:05 PM, Jorgen Simonsen <jorgen589_at_gmail.com> wrote:
> Hi all,
> I have performed a simulation and some of the states from the simulation I
> would like to start from those conformations. So the protein has diffused a
> little bit so it is no longer in the center of the simulation box. I do not
> have the restart files for all of the states that I would like to start a
> new simulation from - it is possible to start the simulation from the vmd
> snapshot and put in new values for center of box as well as box size for PME
> and PBC? I have a hard time to reproduce the number of water molecules if I
> just take the protein and redo the solvation process along with
> minimization.
> Thanks in advance

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