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
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
