[gmx-users] Pressure Fluactiation
Hİ all, I ran simulation of pvdf(ligand) in solution. My problem is pressure fluctuation, My system's pressure fluctuated around reference pressure and average pressure is not equal to my reference pressure. I did well minimisation and nvt run for system before npt run. What should i do about average pressure and reference pressure non-equality? I want to control system pressure because I research about pressure depended potential across the box behavour of the pvdf. Thank you. -- 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 Fluactiation
Hi, It's hard to say anything in the absence of any numbers about average or fluctuations. Do check out http://www.gromacs.org/Documentation/Terminology/Pressure Mark On Wed, Nov 22, 2017 at 9:59 PM ali akgün wrote: > Hİ all, > > I ran simulation of pvdf(ligand) in solution. My problem is pressure > fluctuation, My system's pressure fluctuated around reference pressure and > average pressure is not equal to my reference pressure. I did well > minimisation and nvt run for system before npt run. What should i do about > average pressure and reference pressure non-equality? I want to control > system pressure because I research about pressure depended potential across > the box behavour of the pvdf. > > Thank you. > -- > 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 Fluactiation
Hİ, Thank you for reply but can i minimize fluctuation? On Wed, Nov 22, 2017 at 11:05 PM, Mark Abraham wrote: > Hi, > > It's hard to say anything in the absence of any numbers about average or > fluctuations. Do check out > http://www.gromacs.org/Documentation/Terminology/Pressure > > Mark > > On Wed, Nov 22, 2017 at 9:59 PM ali akgün wrote: > > > Hİ all, > > > > I ran simulation of pvdf(ligand) in solution. My problem is pressure > > fluctuation, My system's pressure fluctuated around reference pressure > and > > average pressure is not equal to my reference pressure. I did well > > minimisation and nvt run for system before npt run. What should i do > about > > average pressure and reference pressure non-equality? I want to control > > system pressure because I research about pressure depended potential > across > > the box behavour of the pvdf. > > > > Thank you. > > -- > > 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. -- 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 Fluactiation
Yes, by running longer, or on a larger system, just as statistical mechanics predicts. Mark On Wed, Nov 22, 2017 at 10:16 PM ali akgün wrote: > Hİ, > Thank you for reply but can i minimize fluctuation? > > On Wed, Nov 22, 2017 at 11:05 PM, Mark Abraham > wrote: > > > Hi, > > > > It's hard to say anything in the absence of any numbers about average or > > fluctuations. Do check out > > http://www.gromacs.org/Documentation/Terminology/Pressure > > > > Mark > > > > On Wed, Nov 22, 2017 at 9:59 PM ali akgün > wrote: > > > > > Hİ all, > > > > > > I ran simulation of pvdf(ligand) in solution. My problem is pressure > > > fluctuation, My system's pressure fluctuated around reference pressure > > and > > > average pressure is not equal to my reference pressure. I did well > > > minimisation and nvt run for system before npt run. What should i do > > about > > > average pressure and reference pressure non-equality? I want to control > > > system pressure because I research about pressure depended potential > > across > > > the box behavour of the pvdf. > > > > > > Thank you. > > > -- > > > 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. > -- > 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 Fluactiation
I will run with bigger nsteps (like monte carlo :D) , thank you for reply sir. On Wed, Nov 22, 2017 at 11:17 PM, Mark Abraham wrote: > Yes, by running longer, or on a larger system, just as statistical > mechanics predicts. > > Mark > > On Wed, Nov 22, 2017 at 10:16 PM ali akgün > wrote: > > > Hİ, > > Thank you for reply but can i minimize fluctuation? > > > > On Wed, Nov 22, 2017 at 11:05 PM, Mark Abraham > > > wrote: > > > > > Hi, > > > > > > It's hard to say anything in the absence of any numbers about average > or > > > fluctuations. Do check out > > > http://www.gromacs.org/Documentation/Terminology/Pressure > > > > > > Mark > > > > > > On Wed, Nov 22, 2017 at 9:59 PM ali akgün > > wrote: > > > > > > > Hİ all, > > > > > > > > I ran simulation of pvdf(ligand) in solution. My problem is pressure > > > > fluctuation, My system's pressure fluctuated around reference > pressure > > > and > > > > average pressure is not equal to my reference pressure. I did well > > > > minimisation and nvt run for system before npt run. What should i do > > > about > > > > average pressure and reference pressure non-equality? I want to > control > > > > system pressure because I research about pressure depended potential > > > across > > > > the box behavour of the pvdf. > > > > > > > > Thank you. > > > > -- > > > > 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. > > -- > > 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. > -- 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.
