[gmx-users] Regarding using random seed

Thu Mar 10 16:00:00 CET 2016

On 3/10/16 3:21 AM, neha chaudhary wrote:
> Hello Sir,
>
> Thanks for your help.
>
> I need to clear one more doubt, if I am performing MD simulations with the
> mentioned parameter set but using same initial structures then will it
> affect the reproducibility of the results.
> Actually, I have repeated MD simulations for my protein-ligand complex
> three times but I have taken the same initial structure every time using
> the same parameters while performing NVT simulations followed by NPT and MD
> run (gen-vel = no in npt.mdp and md.mdp file). Is this procedure correct if
> I want to testify the reliability of my results.
>

"Reliability" and "reproducibility" are different things.  Your results are 
reliable if you have (1) a sound physical model, (2) application of appropriate 
algorithms, and (3) sufficient sampling.  Running multiple simulations addresses 
point 3 but not the other two.  Reproducibility means you get the same average 
behavior, so that's related to point 3, but that does not mean that everything 
will be exactly the same (or even that the same .tpr will necessarily generate 
binary identical trajectories; see the GROMACS website for discussion on this 
topic).

-Justin

> continuation = no
> gen-vel = yes
> gen-seed = -1
>
>
> Best Regards,
>
> *Neha*
>
> Research Scholar,
> Centre for Computational Biology and Bioinformatics,
> School of Life Sciences,
> Central University of Himachal Pradesh,
>
>
>
>
>
> On Wed, Mar 9, 2016 at 6:36 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
>
>> Right!
>>
>> T.
>> On Mar 9, 2016 12:24 PM, "neha chaudhary" <nehachaudhary769 at gmail.com>
>> wrote:
>>
>>> Hi,
>>>
>>> So all I have to do is to extract different configurations from my
>> already
>>> performed MD simulation. Then I have to prepare a new system using that
>>> configuration with the following parameters and rerun the simulations:
>>>
>>> continuation = no
>>> gen_vel = yes
>>> gen-seed = -1
>>>
>>> Right?
>>>
>>>
>>> Best Regards,
>>>
>>> *Neha*
>>>
>>> Research Scholar,
>>> Centre for Computational Biology and Bioinformatics,
>>> School of Life Sciences,
>>> Central University of Himachal Pradesh,
>>>
>>>
>>>
>>>
>>>
>>> On Wed, Mar 9, 2016 at 4:06 PM, Tsjerk Wassenaar <tsjerkw at gmail.com>
>>> wrote:
>>>
>>>> Hi Neha,
>>>>
>>>> Set
>>>>
>>>> continuation = no
>>>> gen_vel = yes
>>>>
>>>> (check http://manual.gromacs.org/online/mdp_opt.html#vel)
>>>>
>>>> Best,
>>>>
>>>> Tsjerk
>>>>
>>>>
>>>> On Wed, Mar 9, 2016 at 11:16 AM, neha chaudhary <
>>>> nehachaudhary769 at gmail.com>
>>>> wrote:
>>>>
>>>>> Thanks Tsjerk for replying,
>>>>>
>>>>> I want to ask one more question that to start with new velocities,
>> what
>>>>> changes I have to make and in which .mdp file?
>>>>>
>>>>> Best Regards,
>>>>>
>>>>> *Neha*
>>>>>
>>>>> Research Scholar,
>>>>> Centre for Computational Biology and Bioinformatics,
>>>>> School of Life Sciences,
>>>>> Central University of Himachal Pradesh,
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Wed, Mar 9, 2016 at 3:37 PM, Tsjerk Wassenaar <tsjerkw at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> Hi Neha,
>>>>>>
>>>>>> You can perform a simulation first, and then extract
>> configurations,
>>>>> which
>>>>>> you simulate with new starting velocities. Alternatively, you can
>>>>> generate
>>>>>> a number of different starting structures using elastic-network
>>>> modeling,
>>>>>> like with the ElNemo server. Mind to first energy minimize the
>>>> resulting,
>>>>>> extrapolated structures, as they may be stretchedhere and there.
>>>>>>
>>>>>> Hope it helps,
>>>>>>
>>>>>> Tsjerk
>>>>>>
>>>>>> On Wed, Mar 9, 2016 at 10:54 AM, neha chaudhary <
>>>>>> nehachaudhary769 at gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>>> Hello there,
>>>>>>>
>>>>>>>
>>>>>>> Can anyone tell me how can I start my MD simulations with
>> different
>>>>>>> starting structure (random seed) for my protein-ligand complex.
>>> Can I
>>>>>> start
>>>>>>> with different sets of coordinates and velocities? If yes, how?
>>>>>>>
>>>>>>>
>>>>>>> Thanks,
>>>>>>>
>>>>>>> *Neha*
>>>>>>> Research Scholar,
>>>>>>> Centre for Computational Biology and Bioinformatics,
>>>>>>> School of Life Sciences,
>>>>>>> Central University of Himachal Pradesh,
>>>>>>> --
>>>>>>> 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.
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Tsjerk A. Wassenaar, Ph.D.
>>>>>> --
>>>>>> 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.
>>>>>>
>>>>> --
>>>>> 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.
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Tsjerk A. Wassenaar, Ph.D.
>>>> --
>>>> 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.
>>>>
>>> --
>>> 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.
>>>
>> --
>> 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.
>>

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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