[gmx-users] Possible to stop mdrun changing file names when usingcheckpoint files?

[Dallas B. Warren]

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?

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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