[gmx-users] Rupture force definition
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.
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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