[gmx-users] Rupture force definition
rockinbhu at gmail.com
Mon Jun 25 14:48:32 CEST 2018
I have observed one thing that during pulling (Constant velocity pulling )
of dsDNA/dsRNA ( globally say Nucleic acid ) along helical direction, we
observe that in the force/time .xvg file, some time force value is +ve and
some time force value is -ve. So why it happens. In my thinking it should
always be +ve.
On Mon, Jun 11, 2018 at 5:37 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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
>> 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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* Rakesh Kumar Mishra*
* (RA)CSD SINP Kolkata, India*
*E-mail - rakesh.mishra at saha.ac.in <rakesh.mishra at saha.ac.in> *
*Phone n. +91 9473662491, +91877749632*
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