Thank you very much Justin for your reply -----Mensaje original----- De: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> En nombre de Justin Lemkul Enviado el: miércoles, 14 de noviembre de 2018 14:51 Para: gmx-us...@gromacs.org Asunto: Re: [gmx-users] pcoupl Berendsen
On 11/14/18 5:28 AM, Gonzalez Fernandez, Cristina wrote: > Hi Justin, > > I have taken a few days in answering you because I was trying to reduce the > discrepancies between the pressure I obtain after simulation and the one I > set in the .mdp file. However, I have no achieve very good results. As I > indicated in the previous email, in my simulations ref_p=1bar and ref_t=298K. > According to the output of gmx energy, the pressure average after the > simulation is 0.19bar , Err.est= 0.59 and RMSD=204,98; and for the > temperature average=298.003, Err.est=0,0032; RMSD=2,76. > > From this results and your previous email, as the error (Err.est) in > the pressure is of the same magnitude as the That error estimate is not relevant here. Your reported pressure is 0.19 ± 205, which is indistinguishable from the target pressure of 1. -Justin > pressure value after simulation, the pressure significantly differs from the > reference value (1bar), so for example, more simulation time will be > required. This is also supported by the high RMSD, which is in the order of > hundreds. For the temperature, the error is 5 orders of magnitude lower than > the obtained value and the RMSD is very low. This suggests that the system > has reach the equilibrium temperature. Are these reasons correct? > > Another thing that makes me think that the pressure I obtain is not correct > is that the pressure I obtained after simulation and the one I obtain after > analysis also differ significantly (0.19 and 3.9 bar respectively). > > I have used long both NPT equilibration and simulation times (50 ns) and the > results are similar to the ones I have indicated above, which apparently > means that the system is stable. > > > From these discrepancies, do you think the differences are not as important > as I am considering?, what could I do to obtain more accurate pressure values? > > Regarding the Parrinello-Rahnman is "not stable for low pressures", I > understood that when using low pressures obtaining the reference pressure is > sometimes difficult by using Parrinello-Rahman. I was trying to use this > article in order to explain why my simulation pressures differ from the > ref_p, but as you say, I have also read papers that use Parrinello-Rahman for > simulating 1bar systems. > > Thank you very much for all your help, > > C. > > > -----Mensaje original----- > De: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> En nombre de > Justin Lemkul Enviado el: jueves, 8 de noviembre de 2018 14:01 > Para: gmx-us...@gromacs.org > Asunto: Re: [gmx-users] pcoupl Berendsen > > > > On 11/8/18 7:50 AM, Gonzalez Fernandez, Cristina wrote: >> Dear Gromacs users, >> >> In my simulations, I have specified ref_p= 1bar but after MD >> simulation I obtain pressures equal to 0.19 bar (even > A pressure without an error bar is a meaningless value. The fluctuations of > pressure in most systems are on the order of tens or hundreds of bar, meaning > your result is indistinguishable from the target value. > >> with long simulation times) when using pcoupl=Parrinello-Rahman. I >> know that Parrinello-Rahman is recommend for production runs and >> Berendsen for NPT equilibration. However, I have read in an article >> that Parrinello-Rahman is not stable for low pressures, so in such >> situations its better to use Berendsen. I have tried to use Berendsen >> for > I would be interested to know how this "not stable for low pressures" > was determined, because it seems completely unlikely to be true. Most > MD simulations nowadays use Parrinello-Rahman for pressure coupling at > 1 > bar/1 atm without any issue if the system is properly equilibrated (and if > not, the problem is with preparation, not the barostat itself). > >> MD simulation but I obtain this Warning and I cannot remove it with the >> -maxwarn option. >> >> "Using Berendsen pressure coupling invalidates the true ensemble for the >> thermostat" >> >> >> How can I use Berendsen for MD simulation? > Simply, you can't, and you shouldn't. The Berendsen method produces an > invalid statistical mechanical ensemble. It relaxes systems quickly and is > therefore still useful for equilibration, but should never be employed during > data collection. Full stop. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > 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. -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== -- 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. -- 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.
