[gmx-users] Rupture force definition

Justin Lemkul jalemkul at vt.edu
Mon Jun 11 14:08:05 CEST 2018

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 

> 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 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


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