[gmx-users] Assignment of new velocities for multi-runs
Peter C. Lai
pcl at uab.edu
Sat Sep 29 09:08:20 CEST 2012
If the system is already well equilibrated previously then you can probably
safely reassign velocities during NPT. The best way to do this would probably
be to take the equilibrated checkpoint file as the starting point:
grompp -f genvel-yes-npt.mdp -t previous.cpt ...
You'll still have to wait some ns for the system to reequilibrate so data
comparisons between the runs for the first several ns will not be meaningful,
so ultimately, the question is what you do you hope to gain from reassigning
velocities at the beginning?
On 2012-09-28 11:59:02PM -0700, James Starlight wrote:
> Dear All!
> I'd like to perform several simulations of the membrane protein
> started from the common conditions which differs only in the initial
> velocities ( for each simulation random speed distribution will be
> used from the Maxwell distribution).
> Because I simulate membrane protein the long equilibration phase is
> required for that system. I've noticed that new velocities sets are
> assigned in the NVT phase of equilibration (100ps) after which more
> prolongest npt equilibration (10ns) is followed.
> Does it require that new velocities always be assigned exactly during
> equilibration of my system ? Could I use new velocities in the
> production md run instead ? In the latter case my system will be
> equilibrated with one velocities but further production MD will be
> with another velocities each time? (so in latter case I can avoid long
> equilibration phase for each simulation).
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Peter C. Lai | University of Alabama-Birmingham
Programmer/Analyst | KAUL 752A
Genetics, Div. of Research | 705 South 20th Street
pcl at uab.edu | Birmingham AL 35294-4461
(205) 690-0808 |
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