[gmx-users] Topology file and itp file

[Justin Lemkul]

On 4/22/17 9:06 PM, lan hoa Trinh wrote:
> Dear Justin,
> I don't understand what you meant by saying MD is chaotic. You mean about
> velocity? I know that when we generate velocity based on Boltzmann
> distribution, we have to generate random number. However, what we call
> random numbers is not actually "random" because they are obeying algorithm.
> I don't know if I understand correctly but if we start from an initial
> value, we generate a "seed", and then we have a "random" series of number.
> However next time, when we rerun the simulation, the same series will be
> created.
>

This is not really what I was referring to at all.

http://www.gromacs.org/Documentation/Terminology/Reproducibility

What is not clear from your posts is really how you're assessing "same" vs. 
"different" - you mention potential energy but you do not say what you did.  A 
time series?  A single point energy?  An average of some sort?  If your two 
simulations are too short to be considered converged, you will probably get a 
different value.  Whether that value means anything is an open question.  In the 
limit of ergodicity, a simple system like yours should easily produce the same 
ensemble-average properties.  But if you're just testing whether or not your two 
topologies are the same, the only test you need to do is what I suggested, a 
single-point energy.  Compare apples to apples.  Or atoms to atoms, as it were :)

-Justin

> *Lan Hoa*
>
> 2017-04-21 7:21 GMT-05:00 Justin Lemkul <jalemkul at vt.edu>:
>
>>
>>
>> On 4/20/17 4:37 PM, lan hoa Trinh wrote:
>>
>>> Dear Mark,
>>> I equilibrated my system in NVT, and then plot the potential energy.
>>> However the potential energy created with the two topology is not match.
>>> Thanks in advance,
>>>
>>
>> MD is chaotic, and even identical topologies will yield different
>> results.  If you want to test the equivalence of a topology, you should
>> evaluate a single-point energy of an identical configuration of atoms with
>> the two topologies.  That's the only meaningful test.
>>
>> http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy
>>
>> -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

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