[gmx-users] Rupture force definition

[Rakesh Mishra]

Dear Justin.

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
> interpretations.
>
> 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
>
> --
> ==================================================
>
> 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
> http://www.thelemkullab.com
>
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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*