dear Mr.alizadeh thanks for your reply the repeatability of average pressure is my problem. average pressure isn't repeatability when i repeat NPT simulation stage many times, simulation results are very different for the pressure average. my system is protein-ligand complex. How long do you think is enough for the NPT stage? Regards On , Mahboobeh Eslami <mahboobeh.esl...@yahoo.com> wrote: dear Mr.alizadeh thanks for your reply my problem hasn't good repeatability. when i repeat NPT simulation stage many times, simulation results are very different for the pressure average. my system is protein-ligand complex. How long do you think is enough for the NPT stage? Regards
On Monday, April 28, 2014 12:48 PM, Ali Alizadeh <ali.alizadehmoja...@gmail.com> wrote: Dear Mahboobeh, I do not know what component your system includes. However, based on my experiences, the fluctuation of pressure is high especially for small and incompressible systems. Besides, you should increase your simulation time. You should not expect that the pressure can converge exactly to the pressure you want. I think(I do not know details of your simulations) pressure fluctuation is natural, of course not for short simulations, the average pressure for equilibriated systems is important. ----------------------dear justin Thank you for your reply. My system is about 123,000 atoms and my box is cubic. I'm following conditions apply: pcoupl?????????? = Parrinello-Rahman????? Pcoupltype?????? = Isotropic?????????? tau_p??????????? = 0.5??????????????? compressibility? = 4.5e-5?????????????? ref_p??????????? = 1.0??????????????? refcoord_scaling = com But the average pressure is not good repeatability. To fix this problem I did two NPT simulation stageThe first 100ps by brendsand barostat then 100ps by Parrinello-Rahman barostatbut Still not good repeatability. I frequently change tau_p? but I did not get any results. Increase the NPT simulation time did not solve the problem. I strongly need your help Thank you sincerely for your kindness On Friday, April 25, 2014 5:08 PM, Justin Lemkul <jalem...@vt.edu> wrote: On 4/25/14, 2:36 AM, Mahboobeh Eslami wrote: > hi GMX users > please help me > i want to simulate protein-ligand complex by gromacs4.6.5 > when i repeat NPT simulation stage? many times,? simulation results are very > different for the pressure average.I sincerely thank you for your guidance > Pressure is probably the most ill-defined quantity in MD simulations.? It can fluctuate dramatically.? Without the actual numbers, it's hard to comment, but issues related to pressure have been discussed extensively over the list in the past and there is useful information in http://www.gromacs.org/Documentation/Terminology/Pressure. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 -- Sincerely Ali Alizadeh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.