[gmx-users] Topology file and itp file

[lan hoa Trinh]

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.

*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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