[gmx-users] Rupture force definition

Justin Lemkul jalemkul at vt.edu
Mon Jun 25 15:56:53 CEST 2018



On 6/25/18 8:48 AM, Rakesh Mishra wrote:
> 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.

Free energy surfaces are rugged. Some intermediate conformations may 
result in local free energy wells.

-Justin

> 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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>
>

-- 
==================================================

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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