[gmx-users] Rupture force definition

[Justin Lemkul]

On 6/8/18 2:52 AM, Rakesh Mishra wrote:
> Dear Justin .
> I have  two query
>
> 1-What can be the optimized value of rate can be taken
> for pulling of  dsDNA/dsRNA using gromacs format where solvent is  aqua.
>  From your umbrella sampling manual,  rate is very high like (0.01 nm/ps),
> which is equal to 0.0001Angstrom/fs.

You'll note in the SI we tested lower values and achieved the same 
outcome, so you need to test a few to be sure that whatever pull rate 
you impose does not introduce artifacts. There is no way, a priori, to 
know what an "optimized" rate would be. That term also has multiple 
interpretations.

> 2- In pulling mdp file no random seed is discussed. But if we want to
> obtain 2 or 3 different trajectory during
>       pulling ( of the same system ) for  different seed, then how to give
> different seed in pulling  mdp file.
>
> Note -  In my thinking in gromacs, gen_seed  = -1 is default value.  And it
> comes , when NVT is applied ( where
>               velocity generation is allowed, to achieve required
> temperature through maxwell distribution ). But in case of pulling, where
> no velocity
>               generation is allowed . Then how to calculate different
> pulling simulation of the same system for different seeds.

One does not supply a new random seed when doing a continuation of a 
run. If you want to start new simulations in each window or in multiple 
replicates of a run, then use "gen_seed = -1" to get a completely random 
seed based on the process ID.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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