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 ?? With Best Wishes and Regards, Rama David On Sat, Jul 20, 2013 at 4:49 PM, Justin Lemkul <jalem...@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 >> 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 > > jalemkul@outerbanks.umaryland.**edu <jalem...@outerbanks.umaryland.edu> | > (410) 706-7441 > > ==============================**==================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * 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-requ...@gromacs.org. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- 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
