# [gmx-users] Topology file and itp file

lan hoa Trinh trinhlanhoa at gmail.com
Sun Apr 23 04:39:13 CEST 2017

```Dear Justin,
I am assessing based on a time series. You are right :), even I used the
same topology file, the change over time of the potential energy is still
different. It is good to know ^&^ . All the information you provided are
very helpful. Ok, let me try to express what I 've understood so far:
When we assess a single point energy, if the two topology are the same, we
will get the same value of energy at a single point (which could be the
starting point or an arbitrary point of the trajectory). However, due to
the non-producibility, even we get the same value of energy at each single
point, it is not true when we try to simulate over a period of time and
what we can trust is the the average value.
Hum, do I understand wrongly again, hixx.
Best regards,

*Lan Hoa*

2017-04-22 20:41 GMT-05:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> 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.
>>>>
>>>>
>>> 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
>
> ==================================================
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```