[gmx-users] Rupture force definition
rockinbhu at gmail.com
Fri Jun 8 08:52:14 CEST 2018
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.
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
generation is allowed . Then how to calculate different
pulling simulation of the same system for different seeds.
On Tue, May 15, 2018 at 9:13 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 5/15/18 2:46 AM, Rakesh Mishra wrote:
>> Dear Justin,
>> In all the respect that you have suggested is absolutely correct.
>> But I have a question that just like a constant rate pulling
>> like - [pull_coord1_rate = 0.01 ; 0.01 nm per ps = 10 nm
>> per 1 ns ( which was from your umbrella sampling)]
>> Is there any formate in gromacs for the pulling for force rate like.
>> 0.01 pn per ps/fs (rather than constant force pulling)
> I know of no such formula.
> 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
> Gromacs Users mailing list
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
* 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*
More information about the gromacs.org_gmx-users