[gmx-users] Different temperature

David van der Spoel spoel at xray.bmc.uu.se
Thu Dec 22 20:22:07 CET 2005

Mark Abraham wrote:
> Andrea Carotti wrote:
>> Hi,
>> I've followed  the procedure of a paper that used gromacs for the MD 
>> simulation on the same target I have (same xray starting structure). I 
>> have followed the lines you mentioned:
>> 1) energy minimization to relieve bad contacts after solvation, 
>> followed by
>> 2) position-restrained NPT simulations
>> Do you have some suggestions? do I have to change something or this 
>> temperature can be considered acceptable?
>> In other simulations I have found a good reproducibility of some 
>> published results
> OK, that might be reasonable. I'd still encourage an NVT stage if 
> nothing else works for you. I would check all of the output of grompp 
> and editconf, etc. very carefully for warnings that you haven't paid 
> attention to. I would not consider this temperature behaviour 
> acceptable, and think it likely that there is something wrong with the 
> way you've set up the system. Perhaps it's too obvious, but have a look 
> at the structure at each stage of the preparation process :-)

Reduce tau_T to 0.1 and increase tau_p to 1.0. How about cut-offs etc.?
Heating is mainly a cut-off artifact.

> Mark
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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