[gmx-users] Topology file and itp file

[Justin Lemkul]

On 4/22/17 10:39 PM, lan hoa Trinh wrote:
> 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

Correct.

> 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.

Correct.

-Justin

-- 
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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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