[gmx-users] Different temperature

[Mark Abraham]

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 :-)

Mark