[gmx-users] NPT MD and Berendsen
Dear All, I am using Berendsen barostat and thermostat for NPT equilibration MD run at 1 atm and 300 K. While it runs fine, average pressure at the end of the run is 19 bar. I am confused whether this is way off 1 atm target, or is justified recalling gromacs manual that says Berendsen barostat does not yield correct thermodynamic ensemble. IN addition, initial box elongates to have space at both ends in z-direction as can be seen in following link: https://www.dropbox.com/sh/dahnyy3zy6vb1xh/AAD5ppxrm18rB3DHZ0Qji0qva Again, I am not sure if this is a case for concern or just artifact of using Berendsen. Is Parrinello-Rahman better than Berendsen, even for initial NPT equilibration? Thanks Chetan -- 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] NPT MD and Berendsen
By space in second part of the email, I meant vacuum. Thanks Chetan On Mon, Jun 23, 2014 at 12:50 AM, Chetan Mahajan wrote: > Dear All, > > I am using Berendsen barostat and thermostat for NPT equilibration MD run > at 1 atm and 300 K. While it runs fine, average pressure at the end of the > run is 19 bar. I am confused whether this is way off 1 atm target, or is > justified recalling gromacs manual that says Berendsen barostat does not > yield correct thermodynamic ensemble. > > IN addition, initial box elongates to have space at both ends in > z-direction as can be seen in following link: > > https://www.dropbox.com/sh/dahnyy3zy6vb1xh/AAD5ppxrm18rB3DHZ0Qji0qva > > Again, I am not sure if this is a case for concern or just artifact of > using Berendsen. > > Is Parrinello-Rahman better than Berendsen, even for initial NPT > equilibration? > > Thanks > Chetan > -- 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] NPT MD and Berendsen
How long was the average taken over? If the error is larger than the pressure itself, you cannot make judgment. Generally Berendsen is only inaccurate about the fluctuations, not the mean value. Francis On Mon, Jun 23, 2014 at 1:50 PM, Chetan Mahajan wrote: > Dear All, > > I am using Berendsen barostat and thermostat for NPT equilibration MD run > at 1 atm and 300 K. While it runs fine, average pressure at the end of the > run is 19 bar. I am confused whether this is way off 1 atm target, or is > justified recalling gromacs manual that says Berendsen barostat does not > yield correct thermodynamic ensemble. > > IN addition, initial box elongates to have space at both ends in > z-direction as can be seen in following link: > > https://www.dropbox.com/sh/dahnyy3zy6vb1xh/AAD5ppxrm18rB3DHZ0Qji0qva > > Again, I am not sure if this is a case for concern or just artifact of > using Berendsen. > > Is Parrinello-Rahman better than Berendsen, even for initial NPT > equilibration? > > Thanks > Chetan > -- > 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. > -- Zhifeng (Francis) Jing Graduate Student in Physical Chemistry School of Chemistry and Chemical Engineering Shanghai Jiao Tong University http://sun.sjtu.edu.cn -- 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] NPT MD and Berendsen
thermodynamic ensemble has nothing to do with an average pressure value. Dr. Vitaly V. Chaban On Mon, Jun 23, 2014 at 7:50 AM, Chetan Mahajan wrote: > Dear All, > > I am using Berendsen barostat and thermostat for NPT equilibration MD run > at 1 atm and 300 K. While it runs fine, average pressure at the end of the > run is 19 bar. I am confused whether this is way off 1 atm target, or is > justified recalling gromacs manual that says Berendsen barostat does not > yield correct thermodynamic ensemble. > > IN addition, initial box elongates to have space at both ends in > z-direction as can be seen in following link: > > https://www.dropbox.com/sh/dahnyy3zy6vb1xh/AAD5ppxrm18rB3DHZ0Qji0qva > > Again, I am not sure if this is a case for concern or just artifact of > using Berendsen. > > Is Parrinello-Rahman better than Berendsen, even for initial NPT > equilibration? > > Thanks > Chetan > -- > 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] NPT MD and Berendsen
Thanks. Average was taken over 1000 ps. Error estimate is 2.9 which is smaller than average pressure of 19.87 bar. Here is the complete statistics: Energy Average Err.Est. RMSD Tot-Drift --- Temperature 299.968 0.0131.98625 0.062225 (K) Pressure19.86992.9 726.92413.5906 (bar) Interestingly, average pressure is close to one (0.86 or 0.8 bar) when refcoord scaling of -all is used for position restraints. Above simulation where average pressure is so large was carried out with refcoord-scaling of -com option. I am simulating TiO2 crystal solvated by water, formate and sodium ion. Now, one important observation is that with -com option, crystal slab moves a distance during change of box dimensions in NPT equilibration, whereas slab DOES NOT move with -all option. However, -com option is more favorable since very less water manage to get on the side surfaces of slab compared to that in -all option, where lot of water get on the side which is not desirable. What is happening here? Is it because of slab movement that average pressure is annoyingly large in simulations with -com option? what can be done to rectify or is it okay to proceed anyways? Thanks a lot! regards Chetan On Mon, Jun 23, 2014 at 1:47 AM, Francis Jing wrote: > How long was the average taken over? If the error is larger than the > pressure itself, you cannot make judgment. > Generally Berendsen is only inaccurate about the fluctuations, not the mean > value. > > > Francis > > > On Mon, Jun 23, 2014 at 1:50 PM, Chetan Mahajan > wrote: > > > Dear All, > > > > I am using Berendsen barostat and thermostat for NPT equilibration MD run > > at 1 atm and 300 K. While it runs fine, average pressure at the end of > the > > run is 19 bar. I am confused whether this is way off 1 atm target, or is > > justified recalling gromacs manual that says Berendsen barostat does not > > yield correct thermodynamic ensemble. > > > > IN addition, initial box elongates to have space at both ends in > > z-direction as can be seen in following link: > > > > https://www.dropbox.com/sh/dahnyy3zy6vb1xh/AAD5ppxrm18rB3DHZ0Qji0qva > > > > Again, I am not sure if this is a case for concern or just artifact of > > using Berendsen. > > > > Is Parrinello-Rahman better than Berendsen, even for initial NPT > > equilibration? > > > > Thanks > > Chetan > > -- > > 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. > > > > > > -- > Zhifeng (Francis) Jing > Graduate Student in Physical Chemistry > School of Chemistry and Chemical Engineering > Shanghai Jiao Tong University > http://sun.sjtu.edu.cn > -- > 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] NPT MD and Berendsen
A nonisotropic system will not necessarily end up with exactly the applied pressure -- things like surface tension and stresses/strains end up getting mixed in and throwing things off. On Mon, Jun 23, 2014 at 3:32 PM, Chetan Mahajan wrote: > Thanks. > > Average was taken over 1000 ps. Error estimate is 2.9 which is smaller than > average pressure of 19.87 bar. Here is the complete statistics: > > Energy Average Err.Est. RMSD Tot-Drift > > --- > Temperature 299.968 0.0131.98625 0.062225 (K) > Pressure19.86992.9 726.92413.5906 > (bar) > > Interestingly, average pressure is close to one (0.86 or 0.8 bar) when > refcoord scaling of -all is used for position restraints. Above simulation > where average pressure is so large was carried out with refcoord-scaling of > -com option. I am simulating TiO2 crystal solvated by water, formate and > sodium ion. Now, one important observation is that with -com option, > crystal slab moves a distance during change of box dimensions in NPT > equilibration, whereas slab DOES NOT move with -all option. However, -com > option is more favorable since very less water manage to get on the side > surfaces of slab compared to that in -all option, where lot of water get on > the side which is not desirable. > > What is happening here? Is it because of slab movement that average > pressure is annoyingly large in simulations with -com option? what can be > done to rectify or is it okay to proceed anyways? > > Thanks a lot! > regards > Chetan > > > > On Mon, Jun 23, 2014 at 1:47 AM, Francis Jing > wrote: > > > How long was the average taken over? If the error is larger than the > > pressure itself, you cannot make judgment. > > Generally Berendsen is only inaccurate about the fluctuations, not the > mean > > value. > > > > > > Francis > > > > > > On Mon, Jun 23, 2014 at 1:50 PM, Chetan Mahajan > > wrote: > > > > > Dear All, > > > > > > I am using Berendsen barostat and thermostat for NPT equilibration MD > run > > > at 1 atm and 300 K. While it runs fine, average pressure at the end of > > the > > > run is 19 bar. I am confused whether this is way off 1 atm target, or > is > > > justified recalling gromacs manual that says Berendsen barostat does > not > > > yield correct thermodynamic ensemble. > > > > > > IN addition, initial box elongates to have space at both ends in > > > z-direction as can be seen in following link: > > > > > > https://www.dropbox.com/sh/dahnyy3zy6vb1xh/AAD5ppxrm18rB3DHZ0Qji0qva > > > > > > Again, I am not sure if this is a case for concern or just artifact of > > > using Berendsen. > > > > > > Is Parrinello-Rahman better than Berendsen, even for initial NPT > > > equilibration? > > > > > > Thanks > > > Chetan > > > -- > > > 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. > > > > > > > > > > > -- > > Zhifeng (Francis) Jing > > Graduate Student in Physical Chemistry > > School of Chemistry and Chemical Engineering > > Shanghai Jiao Tong University > > http://sun.sjtu.edu.cn > > -- > > 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] NPT MD and Berendsen
Thank you, Dr. Shirts. My pressure coupling type is also semi-isotropic. So is that simulation worth at all ( since equilibration not on intended pressure even remotely) or we need to discard the simulation totally ? Also, this high pressure (and crystal slab movement ) occurs only with refcoord-scaling option of -com and not with -all. I wonder why. Thanks. regards Chetan On Mon, Jun 23, 2014 at 3:35 PM, Michael Shirts wrote: > A nonisotropic system will not necessarily end up with exactly the applied > pressure -- things like surface tension and stresses/strains end up getting > mixed in and throwing things off. > > > On Mon, Jun 23, 2014 at 3:32 PM, Chetan Mahajan > wrote: > > > Thanks. > > > > Average was taken over 1000 ps. Error estimate is 2.9 which is smaller > than > > average pressure of 19.87 bar. Here is the complete statistics: > > > > Energy Average Err.Est. RMSD Tot-Drift > > > > > --- > > Temperature 299.968 0.0131.98625 0.062225 (K) > > Pressure19.86992.9 726.92413.5906 > > (bar) > > > > Interestingly, average pressure is close to one (0.86 or 0.8 bar) when > > refcoord scaling of -all is used for position restraints. Above > simulation > > where average pressure is so large was carried out with refcoord-scaling > of > > -com option. I am simulating TiO2 crystal solvated by water, formate and > > sodium ion. Now, one important observation is that with -com option, > > crystal slab moves a distance during change of box dimensions in NPT > > equilibration, whereas slab DOES NOT move with -all option. However, -com > > option is more favorable since very less water manage to get on the side > > surfaces of slab compared to that in -all option, where lot of water get > on > > the side which is not desirable. > > > > What is happening here? Is it because of slab movement that average > > pressure is annoyingly large in simulations with -com option? what can be > > done to rectify or is it okay to proceed anyways? > > > > Thanks a lot! > > regards > > Chetan > > > > > > > > On Mon, Jun 23, 2014 at 1:47 AM, Francis Jing > > wrote: > > > > > How long was the average taken over? If the error is larger than the > > > pressure itself, you cannot make judgment. > > > Generally Berendsen is only inaccurate about the fluctuations, not the > > mean > > > value. > > > > > > > > > Francis > > > > > > > > > On Mon, Jun 23, 2014 at 1:50 PM, Chetan Mahajan > > > wrote: > > > > > > > Dear All, > > > > > > > > I am using Berendsen barostat and thermostat for NPT equilibration MD > > run > > > > at 1 atm and 300 K. While it runs fine, average pressure at the end > of > > > the > > > > run is 19 bar. I am confused whether this is way off 1 atm target, or > > is > > > > justified recalling gromacs manual that says Berendsen barostat does > > not > > > > yield correct thermodynamic ensemble. > > > > > > > > IN addition, initial box elongates to have space at both ends in > > > > z-direction as can be seen in following link: > > > > > > > > https://www.dropbox.com/sh/dahnyy3zy6vb1xh/AAD5ppxrm18rB3DHZ0Qji0qva > > > > > > > > Again, I am not sure if this is a case for concern or just artifact > of > > > > using Berendsen. > > > > > > > > Is Parrinello-Rahman better than Berendsen, even for initial NPT > > > > equilibration? > > > > > > > > Thanks > > > > Chetan > > > > -- > > > > 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. > > > > > > > > > > > > > > > > -- > > > Zhifeng (Francis) Jing > > > Graduate Student in Physical Chemistry > > > School of Chemistry and Chemical Engineering > > > Shanghai Jiao Tong University > > > http://sun.sjtu.edu.cn > > > -- > > > 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. >
