[gmx-users] Rupture force definition

[Justin Lemkul]

On 5/17/19 6:15 AM, Rakesh Mishra wrote:
> Dear Justin
>
> After long time again I want to ask one question.
> If suppose I want to repeat the same production
> simulation ( final md simulation) for different seeds,
> then how to do. Because as from the knowledge of
> gromacs there is no manual way to put different seeds
> in the .mdp files.

gen-seed gives you different starting velocities. If you want to perform 
independent simulations they need to either start from (1) different 
velocities, (2) different conformations, or (3) different pull vectors.

-Justin

>
> On Mon, Jun 25, 2018 at 7:27 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> 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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>

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

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================