[gmx-users] Pressure coupling constants
Hi all I am using NPT ensemble to relax a highly compressed system. I find that the way it relaxes depends on the pressure coupling constant ( berendsen barostat). My question is if the choice of the coupling constant would depend on the system conditions? The compressed system would tend to at expand faster rate and accordingly one should use a coupling constant much smaller than usual? Thanks Santo - K. P. Santo Post doctoral fellow Department of Chemistry University of North Carolina at Chapel Hill Chapel Hill, NC, USA -- View this message in context: http://gromacs.5086.x6.nabble.com/Pressure-coupling-constants-tp5013292.html Sent from the GROMACS Users Forum mailing list archive at Nabble.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.
Re: [gmx-users] Pressure coupling constants
If the goal is to get the system to relax from a compressed state as part of preparation, then berendsen pressure coupling is the best way. However, it is not a physical method -- it overly constraints the volume distribution (which is one of the reasons it's good to force a system into a reasonable state). shorter tau_p and also short tau_t will help the relaxation occur without the simulation blowing up. If you want to get any meaningful physics at equilibration, then use MTTK or Parrinello-Rahman. None of the barostats are physically meaningful for nonequilibrium expansion or compression. On Thu, Dec 12, 2013 at 12:11 PM, kpsanto wrote: > Hi all > I am using NPT ensemble to relax a highly compressed system. I find that > the way it relaxes depends on the pressure coupling constant ( berendsen > barostat). My question is if the choice of the coupling constant would > depend on the system conditions? The compressed system would tend to at > expand faster rate and accordingly one should use a coupling constant much > smaller than usual? > > Thanks > Santo > > - > K. P. Santo > Post doctoral fellow > Department of Chemistry > University of North Carolina at Chapel Hill > Chapel Hill, NC, USA > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Pressure-coupling-constants-tp5013292.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.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.
Re: [gmx-users] Pressure coupling constants
Hi Thanks a lot. But if one wants to simulate the sudden expansion (in a crude way ,of course) smaller coupling constant would be more appropriate. Isn't it? santo - K. P. Santo Post doctoral fellow Department of Chemistry University of North Carolina at Chapel Hill Chapel Hill, NC, USA -- View this message in context: http://gromacs.5086.x6.nabble.com/Pressure-coupling-constants-tp5013292p5013300.html Sent from the GROMACS Users Forum mailing list archive at Nabble.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.
Re: [gmx-users] Pressure coupling constants
The most physical thing would be to prepare a system in a small NVT box, then make the box bigger along one dimension, then do an NVT simulation of that system and see what happens along that dimension over time. Barostats are simply not designed to do nonequilibrium right. They magically create volume at all points in the box simultaneously. An equilibrium simulation doesn't care where in the box the volume appears; a nonequilibrium simulation very much does. On Thu, Dec 12, 2013 at 4:01 PM, kpsanto wrote: > Hi > Thanks a lot. But if one wants to simulate the sudden expansion (in a crude > way ,of course) smaller coupling constant would be more appropriate. Isn't > it? > > santo > > - > K. P. Santo > Post doctoral fellow > Department of Chemistry > University of North Carolina at Chapel Hill > Chapel Hill, NC, USA > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Pressure-coupling-constants-tp5013292p5013300.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.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.
Re: [gmx-users] Pressure coupling constants
guess that right! but why do you think NVT scaling of velocities is physical which should also affect the non-equilibrium expansion process? thanks in advance Santo - K. P. Santo Post doctoral fellow Department of Chemistry University of North Carolina at Chapel Hill Chapel Hill, NC, USA -- View this message in context: http://gromacs.5086.x6.nabble.com/Pressure-coupling-constants-tp5013292p5013303.html Sent from the GROMACS Users Forum mailing list archive at Nabble.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.
Re: [gmx-users] Pressure coupling constants
You're right, NVE would probably be better! Otherwise, you would not get expansionary cooling. On Thu, Dec 12, 2013 at 7:08 PM, kpsanto wrote: > guess that right! but why do you think NVT scaling of velocities is physical > which should also affect the non-equilibrium expansion process? > > thanks in advance > Santo > > - > K. P. Santo > Post doctoral fellow > Department of Chemistry > University of North Carolina at Chapel Hill > Chapel Hill, NC, USA > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Pressure-coupling-constants-tp5013292p5013303.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.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.
Re: [gmx-users] Pressure coupling constants
got you. Thanks again! Santo - K. P. Santo Post doctoral fellow Department of Chemistry University of North Carolina at Chapel Hill Chapel Hill, NC, USA -- View this message in context: http://gromacs.5086.x6.nabble.com/Pressure-coupling-constants-tp5013292p5013308.html Sent from the GROMACS Users Forum mailing list archive at Nabble.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.
