[gmx-users] Relation between bonds and nstlist

[Mario Fernández Pendás]

Yes, that is exactly the case, I am using a modified mdrun.

I was using nstlist = 1, but I was testing with different numbers to see
its influence, but I was not sure at wich level it was modifying my results.

Thank you very much.

2014-11-07 22:24 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> On 11/7/14 8:06 AM, Mario Fernández Pendás wrote:
>
>> Hi,
>>
>> Thank you for your reference Nizar, I will read it carefully.
>>
>> Justin, the problem is that I am using my own version of the code with
>> Hybrid Monte Carlo included. Now I am observing that there is a relation
>> between the value of nstlist and the acceptance rate and accuracy of the
>> HMC, so I was trying to guess in which part of the simulation this value
>> is
>> playing a key role.
>>
>>
> So I'm assuming you're using a modified mdrun as your MC engine, then?  If
> that's the case, I would assume you'd probably have to set nstlist = 1 for
> anything to make sense.  If you're making MC moves but not updating the
> neighborlist every time you do, you'd probably end up calculating a bunch
> of spurious stuff.
>
> -Justin
>
>
>  Thank you very much,
>> Mario Fernández-Pendás
>> El 07/11/2014 13:42, "Justin Lemkul" <jalemkul at vt.edu> escribió:
>>
>>
>>>
>>> On 11/7/14 6:23 AM, Mario Fernández Pendás wrote:
>>>
>>>  Dear all,
>>>>
>>>> Is it possible that the choice of the value of nstlist can have any
>>>> influence in the behaviour of the bonds between atoms?
>>>>
>>>>
>>>>  Highly unlikely.  Any atoms participating in bonds or angles have their
>>> nonbonded interactions excluded.  Dihedrals (1-4 interactions) are
>>> usually
>>> included as normal or scaled nonbonded interactions, but occur at a
>>> distance usually within rlist, so the calculation of those interactions
>>> should not be affected by nstlist.
>>>
>>> Can you describe more exactly the problem you're having?  There are a
>>> number of variables at play so it's hard to guess.
>>>
>>> -Justin
>>>
>>> --
>>> ==================================================
>>>
>>> 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
>>>
>>> ==================================================
>>> --
>>> 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
>
> ==================================================
> --
> 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.
>