[gmx-users] Comparing the simulation

Justin Lemkul jalemkul at vt.edu
Sat Jul 20 13:19:21 CEST 2013

On 7/20/13 5:27 AM, rama david wrote:
> Dear Friends,
>                       I did the Simulation study for self
> assembly of peptides . ( I used G96 53a6 FF )
> In First Experiment, I put the two XX peptide far from each other 2.0 nm,
>   and run the simulation.
> In the second experiment I put the two YY peptide seperated by 2.0 nm.
> and run the simulation.
>    In nvt I used the sane parameter, but In NPT, MD simulation I run
> the Parrinello-Rahman barostat with tau_P 2.0 ns for XX peptide and tau_P 1
> for
> YY peptide.
>    I found that peptide YY interaction start at 80ns and XX interaction
> start at 10 ns.
>     I have following Question.
>   1>.        Is it possible to compare  two MD simulation which used the
> same barostat   but having the different tau_P ( Relaxation time).

You'll have to examine pressure distributions very carefully, but I am 
inherently suspicious of trying to salvage results that were based on a mistake.

> 2>.         Could I make the interpretation that  XX peptide start interact
> more early   than YY ??

Based on one simulation of each?  No.

> 3>>. Would we compare  the result between the simulation that uses the
> different barostat ant thermostat but still using the same Force field.

If you are altering both thermostat and barostat, I would be extremely skeptical 
of the results.  Apply consistent methods.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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