Re: [gmx-users] Parrinello-Rahman with surface-tension coupling
Thanks for the advice, Mark! I did exactly this experiment with the same expectations before posting my query. I didn't get any complaint neither from grompp nor from mdrun, what doesn't necessarily mean that this combination is implemented. I just noticed that during equilibration results deteriorate, i.e., the normal pressure which already was close to the target value gets negative, and the surface tension increases significantly over the target value. This could of course be an effect of the different pressure coupling method used. Kind regards, Felipe On 08/14/2012 07:28 AM, Mark Abraham wrote: On 13/08/2012 7:21 PM, Felipe Pineda, PhD wrote: Dear All, the Gromacs User Manual V.4.5.4 states on p. 33: (...) the surface tension and the z-component of the pressure can be coupled to a pressure bath. Presently, this only works with the Berendsen pressure coupling algorithm in GROMACS. My question: does this hold for V. 4.5.5 as well? Is it possible to use the combination: pcoupl= Parrinello-Rahman pcoupltype = surface-tension in an mdp file for a NPgammaT MD run? Probably, but you should try it and see :-) Likely grompp will complain if it is not implemented. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
[gmx-users] Parrinello-Rahman with surface-tension coupling
Dear All, the Gromacs User Manual V.4.5.4 states on p. 33: (...) the surface tension and the z-component of the pressure can be coupled to a pressure bath. Presently, this only works with the Berendsen pressure coupling algorithm in GROMACS. My question: does this hold for V. 4.5.5 as well? Is it possible to use the combination: pcoupl= Parrinello-Rahman pcoupltype = surface-tension in an mdp file for a NPgammaT MD run? Your help and comments will be greatly appreciated. Best regards, Felipe -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
Re: [gmx-users] Parrinello-Rahman with surface-tension coupling
On 13/08/2012 7:21 PM, Felipe Pineda, PhD wrote: Dear All, the Gromacs User Manual V.4.5.4 states on p. 33: (...) the surface tension and the z-component of the pressure can be coupled to a pressure bath. Presently, this only works with the Berendsen pressure coupling algorithm in GROMACS. My question: does this hold for V. 4.5.5 as well? Is it possible to use the combination: pcoupl= Parrinello-Rahman pcoupltype = surface-tension in an mdp file for a NPgammaT MD run? Probably, but you should try it and see :-) Likely grompp will complain if it is not implemented. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
