[gmx-users] Re: NPT simulation for mutation study (Justin A. Lemkul)

[Justin A. Lemkul]

Shyno Mathew wrote:
> Hey Justin,
> 
> thanks for your reply.
> For gen_vel, the manual says "Generate velocities in grompp according to 
> a Maxwell distribution at temperature gen_temp [K], with random seed 
> gen_seed. This is only meaningful with integrator
> md"
> Since the integrator I am using is sd, I put 'gen_vel no'

Ah, I guess I missed that before.

> Yes you are correct, this is equilibration.
>  From what you are saying, even with sd as the integrator, I guess, I 
> should put
> gen_vel       yes
> gen_temp   310  ; i want to do the simulation at 310K
> 

As I said before, you've changed too many variables simultaneously (not very 
scientific ;) to pinpoint exactly what the problem is.  Systematic changes, as 
prescribed by your force field and chosen algorithms, are the only suitable way 
to run a simulation.  Right now, it's a pure guess as to what went wrong.

-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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