Germain
It is VERy unclear to me what you mean by "a simulation of about 10
ps step by step with a restart every 5fs". Do you mean that you will
stop every 5 fs, and restart again for another 5 fs and so on until you
reach 10 ps ? Why would you do that ?
I also do not understand what you mean by "compare the one step
run with the dashed run".
Regardless of that, you are basically right about what sander does when
it restarts:
"> I suppose that :
> - when sander start it computes the PME grids
> - if I use algorithm control of the temperature like Langevin or
> Andersen perhaps there is a repeat of the random number chain because of
> the seed is the same for every run.
> - the accuracy of the coordinate and velocities is better in the program
> than in restrt files. Then this might lead to difference between
> trajectories."
but you are using ntt=1 (Berendsen thermostat) so thgere are no random
number sequences for the temperature control.
Indeed, the precision of the restart file is different than the internal
precision during calculations, and different from the dynamics
coordinates in the mdcrd files.
So, please clarify what you want to do and we might be able to help you.
Cheers
adrian
Germain Vallverdu wrote:
> Hello Amber
>
> I would like to know exactly what append when I restart a molecular
> dynamics with sander.
>
> here is an example of my input file, I use AMBER 9 on a Linux system.
> This is a simulation of an organic molecule in a TIP3P water box.
>
> &cntrl
> nstlim=50000, dt=0.001,
> irest=1, ntx=5,
> ntpr=100, ntwr=100, ntwx=0,
> tempi=300.0, temp0=300.0, ntt=1,
> ntb=2, pres0=1.0, ntp=1, taup=2.0,
> ntc=2, ntf=2,
> cut=10.0,
> /
>
> My problem is the following. I would like to do a simulation of about 10
> ps step by step with a restart every 5fs. But if I compare the one step
> run with the dashed run, trajectory are not similar after few steps.
> Then I would like to know what exactly append when Sander starts.
>
> I suppose that :
> - when sander start it computes the PME grids
> - if I use algorithm control of the temperature like Langevin or
> Andersen perhaps there is a repeat of the random number chain because of
> the seed is the same for every run.
> - the accuracy of the coordinate and velocities is better in the program
> than in restrt files. Then this might lead to difference between
> trajectories.
>
> Nevertheless do you think that something like that is possible to do and
> does it exist other process at the beginning of sander ?
>
> Best wishes
>
> Germain
>
--
Dr. Adrian E. Roitberg
Associate Professor
Quantum Theory Project
Department of Chemistry
Senior Editor. Journal of Physical Chemistry
American Chemical Society
University of Florida PHONE 352 392-6972
P.O. Box 118435 FAX 352 392-8722
Gainesville, FL 32611-8435 Email adrian.qtp.ufl.edu
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Received on Sun Jun 01 2008 - 06:07:09 PDT
