[gmx-users] Comparing the simulation
jalemkul at vt.edu
Sat Jul 20 17:04:01 CEST 2013
On 7/20/13 9:12 AM, rama david wrote:
> Dear Justin,
> Thank you for your Prompt Reply.
> I run a at least 4-5 run of each peptide.
> The result are like the xx peptide form beta structure early than yy
> peptide in each run.
> I just used the different tau_P ( relaxation time ) for NPT and MD
> production run.
> XX tau_p = 2 YY tau_p= 1
> NVT parameter are same.
> On these basis can I make the interpretation that XX form beta sheet
> structure early than YY
> though they uses the same barostat but different tau_P ??
I've already expressed by opinion on that in the previous post.
> With Best Wishes and Regards,
> Rama David
> On Sat, Jul 20, 2013 at 4:49 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>> 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
>>> 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
>> 2>. Could I make the interpretation that XX peptide start
>>> 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 <jalemkul at outerbanks.umaryland.edu> |
>> (410) 706-7441
>> gmx-users mailing list gmx-users at gromacs.org
>> * Please search the archive at http://www.gromacs.org/**
>> Support/Mailing_Lists/Search<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-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
Justin A. Lemkul, Ph.D.
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
More information about the gromacs.org_gmx-users