[gmx-users] Relation between bonds and nstlist

[Mario Fernández Pendás]

Hi Justin,

I am sorry to bother you again, can you recommend me any kind of refference
to understand better how the neighbolist update works?

Thank you very much.

Best regards,
Mario

2014-11-08 12:33 GMT+01:00 Mario Fernández Pendás <mariofp77 at gmail.com>:

> 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
>>>>
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>> --
>> ==================================================
>>
>> 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
>>
>> ==================================================
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>> Gromacs Users mailing list
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>
>