[gmx-users] Anisotropic Pressure Coupling
Hello, I've been trying to run a simulation using anisotropic pressure coupling (I want to allow the box to adjust to the right size for a zero-pressure simulation). I am using the following settings in the .mdp file: Pcoupl = Berendsen pcoupltype = anisotropic tau_p= 2.0 compressibility = 4.5e-05 4.5e-05 4.5e-05 0 0 0 ref_p= 0 0 0 0 0 0 I can grompp the mdp file without error, but when I try to execute mdrun on the tpr file, I obtain the following message: Fatal error: Domain decomposition has not been implemented for box vectors that have non-zero components in directions that do not use domain decomposition: ncells = 1 8 1, box vector[2] = -nan -nan 0.00 If I change the pressure coupling to isotropic and delete the spare matrix components from the settings, the simulation runs without error. Am I not properly specifying the parameters? Is there another error that I could be missing? Thank you, Adriaan -- 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] anisotropic pressure coupling
Hi Mark, Thanks for your reply. I want anisotropic coupling because I want to have box shape deformation during simulation. Like what has been done in above mentioned article. I have read the manual already, but I am still in doubt. I am pretty sure it should be anisotropic to allow these deformations. Do you see anything wrong in parameters I have chosen? Please let me know. Cheers On Thu, Sep 15, 2016 at 4:10 AM, Mark Abraham wrote: > Hi, > > If you want isotropic coupling, don't choose anisotropic. Otherwise, please > make sure you read the documentation of the respective .mdp options. > > Mark > > On Mon, Sep 12, 2016 at 5:54 PM Mohsen Ramezanpour < > ramezanpour.moh...@gmail.com> wrote: > > > Hi Everyone, > > > > Please let me know your opinion on this question. Thanks in advance > > > > Mohsen > > > > On Wed, Sep 7, 2016 at 5:35 PM, Mohsen Ramezanpour < > > ramezanpour.moh...@gmail.com> wrote: > > > > > Dear gromacs users, > > > > > > If we are interested in deformation in simulation box shape (*both > angles > > > and lengths*) during simulation for a lipid system, like what has been > > > done in this article (fig 1, fig 2, and fig 3): > > > > > > "Phase behavior of a phospholipid/fatty acid/water mixture studied in > > > atomic detail." > > > http://www.ncbi.nlm.nih.gov/pubmed/16464104 > > > > > > > > > Reading through Gromacs manual: > > > > > > "When the off-diagonal compressibility are set to zero, a rectangular > > box will > > > stay rectangular. Beware that anisotropic scaling can lead to extreme > > > deformation of the simulation box." > > > > > > and discussions in forum like followings: > > > > > > https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx- > > > users/2008-July/035341.html > > > https://www.mail-archive.com/gmx-users@gromacs.org/msg31242.html > > > http://gromacs.org_gmx-users.maillist.sys.kth.narkive.com/ > > > kENAzgnS/pressure-coupling-for-anisotropic-system > > > > > > I am still in doubt of my .mdp file parameters. > > > > > > Considering that I want to apply a pressure of 1 bar to the lipid > system, > > > is it possible to catch the same box deformation? > > > > > > pcoupl = Parrinello-Rahman > > > pcoupltype = anisotropic > > > ref-p = 1.0 1.0 1.0 0.0 0.0 0.0 > > > tau-p= 0.5 0.5 0.5 0.5 0.5 0.5 > > > compressibility = 4.5e-5 4.5e-5 4.5e-5 4.5e-5 4.5e-5 > > 4.5e-5 > > > > > > I chose ref-P as 0 for the last three values to not force the box to > > change > > > At the same time, I chose compressibilities and tau-p the same for all > > > diagonal and non-diagonal values. > > > > > > Thanks in advance for your comments > > > > > > Thanks > > > Mohsen > > > -- > > > *Rewards work better than punishment ...* > > > > > > > > > > > -- > > *Rewards work better than punishment ...* > > -- > > 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. > -- *Rewards work better than punishment ...* -- 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] anisotropic pressure coupling
Hi, If you want isotropic coupling, don't choose anisotropic. Otherwise, please make sure you read the documentation of the respective .mdp options. Mark On Mon, Sep 12, 2016 at 5:54 PM Mohsen Ramezanpour < ramezanpour.moh...@gmail.com> wrote: > Hi Everyone, > > Please let me know your opinion on this question. Thanks in advance > > Mohsen > > On Wed, Sep 7, 2016 at 5:35 PM, Mohsen Ramezanpour < > ramezanpour.moh...@gmail.com> wrote: > > > Dear gromacs users, > > > > If we are interested in deformation in simulation box shape (*both angles > > and lengths*) during simulation for a lipid system, like what has been > > done in this article (fig 1, fig 2, and fig 3): > > > > "Phase behavior of a phospholipid/fatty acid/water mixture studied in > > atomic detail." > > http://www.ncbi.nlm.nih.gov/pubmed/16464104 > > > > > > Reading through Gromacs manual: > > > > "When the off-diagonal compressibility are set to zero, a rectangular > box will > > stay rectangular. Beware that anisotropic scaling can lead to extreme > > deformation of the simulation box." > > > > and discussions in forum like followings: > > > > https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx- > > users/2008-July/035341.html > > https://www.mail-archive.com/gmx-users@gromacs.org/msg31242.html > > http://gromacs.org_gmx-users.maillist.sys.kth.narkive.com/ > > kENAzgnS/pressure-coupling-for-anisotropic-system > > > > I am still in doubt of my .mdp file parameters. > > > > Considering that I want to apply a pressure of 1 bar to the lipid system, > > is it possible to catch the same box deformation? > > > > pcoupl = Parrinello-Rahman > > pcoupltype = anisotropic > > ref-p = 1.0 1.0 1.0 0.0 0.0 0.0 > > tau-p= 0.5 0.5 0.5 0.5 0.5 0.5 > > compressibility = 4.5e-5 4.5e-5 4.5e-5 4.5e-5 4.5e-5 > 4.5e-5 > > > > I chose ref-P as 0 for the last three values to not force the box to > change > > At the same time, I chose compressibilities and tau-p the same for all > > diagonal and non-diagonal values. > > > > Thanks in advance for your comments > > > > Thanks > > Mohsen > > -- > > *Rewards work better than punishment ...* > > > > > > -- > *Rewards work better than punishment ...* > -- > 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] anisotropic pressure coupling
Hi Everyone, Please let me know your opinion on this question. Thanks in advance Mohsen On Wed, Sep 7, 2016 at 5:35 PM, Mohsen Ramezanpour < ramezanpour.moh...@gmail.com> wrote: > Dear gromacs users, > > If we are interested in deformation in simulation box shape (*both angles > and lengths*) during simulation for a lipid system, like what has been > done in this article (fig 1, fig 2, and fig 3): > > "Phase behavior of a phospholipid/fatty acid/water mixture studied in > atomic detail." > http://www.ncbi.nlm.nih.gov/pubmed/16464104 > > > Reading through Gromacs manual: > > "When the off-diagonal compressibility are set to zero, a rectangular box will > stay rectangular. Beware that anisotropic scaling can lead to extreme > deformation of the simulation box." > > and discussions in forum like followings: > > https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx- > users/2008-July/035341.html > https://www.mail-archive.com/gmx-users@gromacs.org/msg31242.html > http://gromacs.org_gmx-users.maillist.sys.kth.narkive.com/ > kENAzgnS/pressure-coupling-for-anisotropic-system > > I am still in doubt of my .mdp file parameters. > > Considering that I want to apply a pressure of 1 bar to the lipid system, > is it possible to catch the same box deformation? > > pcoupl = Parrinello-Rahman > pcoupltype = anisotropic > ref-p = 1.0 1.0 1.0 0.0 0.0 0.0 > tau-p= 0.5 0.5 0.5 0.5 0.5 0.5 > compressibility = 4.5e-5 4.5e-5 4.5e-5 4.5e-5 4.5e-5 4.5e-5 > > I chose ref-P as 0 for the last three values to not force the box to change > At the same time, I chose compressibilities and tau-p the same for all > diagonal and non-diagonal values. > > Thanks in advance for your comments > > Thanks > Mohsen > -- > *Rewards work better than punishment ...* > -- *Rewards work better than punishment ...* -- 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.
[gmx-users] anisotropic pressure coupling
Dear gromacs users, If we are interested in deformation in simulation box shape (*both angles and lengths*) during simulation for a lipid system, like what has been done in this article (fig 1, fig 2, and fig 3): "Phase behavior of a phospholipid/fatty acid/water mixture studied in atomic detail." http://www.ncbi.nlm.nih.gov/pubmed/16464104 Reading through Gromacs manual: "When the off-diagonal compressibility are set to zero, a rectangular box will stay rectangular. Beware that anisotropic scaling can lead to extreme deformation of the simulation box." and discussions in forum like followings: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2008-July/035341.html https://www.mail-archive.com/gmx-users@gromacs.org/msg31242.html http://gromacs.org_gmx-users.maillist.sys.kth.narkive.com/kENAzgnS/pressure-coupling-for-anisotropic-system I am still in doubt of my .mdp file parameters. Considering that I want to apply a pressure of 1 bar to the lipid system, is it possible to catch the same box deformation? pcoupl = Parrinello-Rahman pcoupltype = anisotropic ref-p = 1.0 1.0 1.0 0.0 0.0 0.0 tau-p= 0.5 0.5 0.5 0.5 0.5 0.5 compressibility = 4.5e-5 4.5e-5 4.5e-5 4.5e-5 4.5e-5 4.5e-5 I chose ref-P as 0 for the last three values to not force the box to change At the same time, I chose compressibilities and tau-p the same for all diagonal and non-diagonal values. Thanks in advance for your comments Thanks Mohsen -- *Rewards work better than punishment ...* -- 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.
