[gmx-users] Rupture force definition

[Rakesh Mishra]

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
no velocity
             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
>
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> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
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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*