> Date: Tue, 17 Feb 2009 16:59:42 +1100
> From: [email protected]
> Subject: RE: [gmx-users] Possible to stop mdrun changing file names when
> usingcheckpoint files?
> To: [email protected]
>
> Chris,
>
> > One option is to avoid checkpoint files all together. I personally use
> > a grompp/mdrun cycle of ~2h segments that was historically done in
> > order to utilize the -sort -shuffle options to gromacs 3. I found it
> > simpler to keep on doing the exact same thing in gromacs 4, even
> > though I no longer -sort or -shuffle. It appears to be working fine
> > for me. I suspect that you could do the same type of thing via tpbconv.
>
> Yes, that is what I was doing previously and are continuing to do so with
> some at the moment with 4.0.X I suppose the question is now, is it a more
> continuous simulation to be using the checkpoint files, or does tpbconv with
> the energy and trajectory files provide the same degree of accuracy?
>
The trajectory and energy file do not store all the state variables for all
thermostats and barostats. But resetting these variables introduces
such a small error in most cases that it is negligible.
I think I'll add a -rename (or something like that) flag to mdrun,
so you can control the renaming.
Berk
> Totally unrelated and a little nugget for people that happen to have an
> iPhone or iPod touch, you can get an application called Molecules for free
> that allows you to view .pdb files, download direct from the pdb database or
> from custom location.
>
> Catch ya,
>
> Dr Dallas Warren
> Pharmacy and Pharmaceutical Sciences
> Monash University
>
> A polar bear is a Cartesian bear that has undergone a polar transformation
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