[gmx-users] Re: Re: NPT simulation for mutation study

[Justin A. Lemkul]

Shyno Mathew wrote:
> Hello Prof. David,
> 
> thanks for your reply.
> I will try using isotropic pressure scaling. But still I am not clear 
> why the simulations ran fine with first .mdp file. As mentioned in the 
> previous email only few parameters were different in my .mdp file 
> compared to my advisor's.
> I am just copying those parameters again:
> Parameters that are different in my advisor's file:
> DispCorr                 = Ener
> tau_t                    = 0.20
> compressibility          = 5e-6  5e-6  5e-6  0 0 0
> gen_vel                  = yes
> gen_temp                 = 1
> gen_seed                 = 473529
> can including dispersion corrections for pressure induce such a huge change?
> 

By changing several variables at once, it becomes hard (read: almost impossible) 
to say what caused it.  By also not generating velocities (assuming this is step 
1 in equilibration), you can induce instability.

The real lesson is you shouldn't make haphazard changes or take anything for 
granted as far as settings that "should work."  Spending a few hours reading the 
literature will save you weeks of troubleshooting an elusive problem.

-Justin

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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