Re: [gmx-users] Use NVT to mimic NVE
I mean here seems to say conserved energy is tilde H [ https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2013-August/083330.html ] On Sat, Oct 18, 2014 at 6:44 PM, Johnny Lu wrote: > The conserved energy from g_energy, which I saw someone say is tilde H, > drop more crazily if I use 1s coupling constant. > > On Mon, Oct 13, 2014 at 5:52 PM, Mark Abraham > wrote: > >> Hi, >> >> What is your target observable? What "got worse?" >> >> Mark >> >> On Mon, Oct 13, 2014 at 11:17 PM, Johnny Lu >> wrote: >> >> > The simulation get worse in a new way. >> > >> > I see that thermostat scales velocity and may not fix numerical error in >> > potential energy. >> > >> > On Mon, Oct 13, 2014 at 2:07 PM, Johnny Lu >> wrote: >> > >> > > I just want something that will patch up the energy lost due to >> numerical >> > > error of NVE simulation of the system ran by mixed precision gromacs, >> > > instead of a thermostat. >> > > >> > > I hope the velocity rescaling is sufficiently uncorrelated with the >> > motion >> > > of the protein. >> > > >> > > So far, the simulations ran 2.5 ns, and the fluctuation of total >> energy >> > > seems to be within 1% of total energy, with a 100ps or 1ns coupling >> > > constant. >> > > >> > > May be I should try a 10 ns coupling constant, just to see if the >> > > simulation would go belly up. >> > > >> > > On Mon, Oct 13, 2014 at 11:02 AM, Michael Shirts >> > > wrote: >> > > >> > >> > I guess, if I pick a coupling constant that is just small enough to >> > >> keep the >> > >> energy conserved, I would get a NVT simulation that is as close as a >> NVE >> > >> simulation as possible. >> > >> >> > >> > Is this correct? >> > >> >> > >> Yes, but then at that point the thermostat isn't actually >> > thermostatting. >> > >> The Bussi comment is merely to show that his thermostat correctly >> > reduces >> > >> to Newton's law in the limit, not that it would be useful to run it >> in >> > >> that >> > >> limit. >> > >> >> > >> On Mon, Oct 13, 2014 at 10:28 AM, Johnny Lu >> > >> wrote: >> > >> >> > >> > On page 014101-3, the Bussi paper ( >> > http://dx.doi.org/10.1063/1.2408420) >> > >> > mentioned: "On the other hand, for coupling constant approaching >> > >> > infinity,the Hamiltonian dynamics is recovered." >> > >> > Does that means that for a large enough coupling constant, the >> > >> velocities >> > >> > are nearly not rescaled, and the dynamics (like rate of motion) >> would >> > be >> > >> > same as that of NVE? >> > >> > >> > >> > A larger coupling constant, means a smaller diffusion coefficient >> in >> > the >> > >> > axillary dynamics by equation 6. >> > >> > >> > >> > While the effects of the velocity rescaling at each step will >> > >> accumulate, a >> > >> > larger coupling constant means the thermostat perturb less of the >> > >> dynamics, >> > >> > and the resulting dynamics is closer to a NVE simulation. >> > >> > There is no worry that the thermostat would suddenly rescale the >> > >> dynamics >> > >> > every x step, because in the procedure of the thermostat, the >> > velocities >> > >> > are rescaled every step, regardless of the coupling constant. >> > >> > >> > >> > I guess, if I pick a coupling constant that is just small enough to >> > keep >> > >> > the energy conserved, I would get a NVT simulation that is as close >> > as a >> > >> > NVE simulation as possible. >> > >> > >> > >> > Is this correct? >> > >> > -- >> > >> > 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/
Re: [gmx-users] Use NVT to mimic NVE
The conserved energy from g_energy, which I saw someone say is tilde H, drop more crazily if I use 1s coupling constant. On Mon, Oct 13, 2014 at 5:52 PM, Mark Abraham wrote: > Hi, > > What is your target observable? What "got worse?" > > Mark > > On Mon, Oct 13, 2014 at 11:17 PM, Johnny Lu > wrote: > > > The simulation get worse in a new way. > > > > I see that thermostat scales velocity and may not fix numerical error in > > potential energy. > > > > On Mon, Oct 13, 2014 at 2:07 PM, Johnny Lu > wrote: > > > > > I just want something that will patch up the energy lost due to > numerical > > > error of NVE simulation of the system ran by mixed precision gromacs, > > > instead of a thermostat. > > > > > > I hope the velocity rescaling is sufficiently uncorrelated with the > > motion > > > of the protein. > > > > > > So far, the simulations ran 2.5 ns, and the fluctuation of total energy > > > seems to be within 1% of total energy, with a 100ps or 1ns coupling > > > constant. > > > > > > May be I should try a 10 ns coupling constant, just to see if the > > > simulation would go belly up. > > > > > > On Mon, Oct 13, 2014 at 11:02 AM, Michael Shirts > > > wrote: > > > > > >> > I guess, if I pick a coupling constant that is just small enough to > > >> keep the > > >> energy conserved, I would get a NVT simulation that is as close as a > NVE > > >> simulation as possible. > > >> > > >> > Is this correct? > > >> > > >> Yes, but then at that point the thermostat isn't actually > > thermostatting. > > >> The Bussi comment is merely to show that his thermostat correctly > > reduces > > >> to Newton's law in the limit, not that it would be useful to run it in > > >> that > > >> limit. > > >> > > >> On Mon, Oct 13, 2014 at 10:28 AM, Johnny Lu > > >> wrote: > > >> > > >> > On page 014101-3, the Bussi paper ( > > http://dx.doi.org/10.1063/1.2408420) > > >> > mentioned: "On the other hand, for coupling constant approaching > > >> > infinity,the Hamiltonian dynamics is recovered." > > >> > Does that means that for a large enough coupling constant, the > > >> velocities > > >> > are nearly not rescaled, and the dynamics (like rate of motion) > would > > be > > >> > same as that of NVE? > > >> > > > >> > A larger coupling constant, means a smaller diffusion coefficient in > > the > > >> > axillary dynamics by equation 6. > > >> > > > >> > While the effects of the velocity rescaling at each step will > > >> accumulate, a > > >> > larger coupling constant means the thermostat perturb less of the > > >> dynamics, > > >> > and the resulting dynamics is closer to a NVE simulation. > > >> > There is no worry that the thermostat would suddenly rescale the > > >> dynamics > > >> > every x step, because in the procedure of the thermostat, the > > velocities > > >> > are rescaled every step, regardless of the coupling constant. > > >> > > > >> > I guess, if I pick a coupling constant that is just small enough to > > keep > > >> > the energy conserved, I would get a NVT simulation that is as close > > as a > > >> > NVE simulation as possible. > > >> > > > >> > Is this correct? > > >> > -- > > >> > 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.o
Re: [gmx-users] Use NVT to mimic NVE
Hi, What is your target observable? What "got worse?" Mark On Mon, Oct 13, 2014 at 11:17 PM, Johnny Lu wrote: > The simulation get worse in a new way. > > I see that thermostat scales velocity and may not fix numerical error in > potential energy. > > On Mon, Oct 13, 2014 at 2:07 PM, Johnny Lu wrote: > > > I just want something that will patch up the energy lost due to numerical > > error of NVE simulation of the system ran by mixed precision gromacs, > > instead of a thermostat. > > > > I hope the velocity rescaling is sufficiently uncorrelated with the > motion > > of the protein. > > > > So far, the simulations ran 2.5 ns, and the fluctuation of total energy > > seems to be within 1% of total energy, with a 100ps or 1ns coupling > > constant. > > > > May be I should try a 10 ns coupling constant, just to see if the > > simulation would go belly up. > > > > On Mon, Oct 13, 2014 at 11:02 AM, Michael Shirts > > wrote: > > > >> > I guess, if I pick a coupling constant that is just small enough to > >> keep the > >> energy conserved, I would get a NVT simulation that is as close as a NVE > >> simulation as possible. > >> > >> > Is this correct? > >> > >> Yes, but then at that point the thermostat isn't actually > thermostatting. > >> The Bussi comment is merely to show that his thermostat correctly > reduces > >> to Newton's law in the limit, not that it would be useful to run it in > >> that > >> limit. > >> > >> On Mon, Oct 13, 2014 at 10:28 AM, Johnny Lu > >> wrote: > >> > >> > On page 014101-3, the Bussi paper ( > http://dx.doi.org/10.1063/1.2408420) > >> > mentioned: "On the other hand, for coupling constant approaching > >> > infinity,the Hamiltonian dynamics is recovered." > >> > Does that means that for a large enough coupling constant, the > >> velocities > >> > are nearly not rescaled, and the dynamics (like rate of motion) would > be > >> > same as that of NVE? > >> > > >> > A larger coupling constant, means a smaller diffusion coefficient in > the > >> > axillary dynamics by equation 6. > >> > > >> > While the effects of the velocity rescaling at each step will > >> accumulate, a > >> > larger coupling constant means the thermostat perturb less of the > >> dynamics, > >> > and the resulting dynamics is closer to a NVE simulation. > >> > There is no worry that the thermostat would suddenly rescale the > >> dynamics > >> > every x step, because in the procedure of the thermostat, the > velocities > >> > are rescaled every step, regardless of the coupling constant. > >> > > >> > I guess, if I pick a coupling constant that is just small enough to > keep > >> > the energy conserved, I would get a NVT simulation that is as close > as a > >> > NVE simulation as possible. > >> > > >> > Is this correct? > >> > -- > >> > 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] Use NVT to mimic NVE
The simulation get worse in a new way. I see that thermostat scales velocity and may not fix numerical error in potential energy. On Mon, Oct 13, 2014 at 2:07 PM, Johnny Lu wrote: > I just want something that will patch up the energy lost due to numerical > error of NVE simulation of the system ran by mixed precision gromacs, > instead of a thermostat. > > I hope the velocity rescaling is sufficiently uncorrelated with the motion > of the protein. > > So far, the simulations ran 2.5 ns, and the fluctuation of total energy > seems to be within 1% of total energy, with a 100ps or 1ns coupling > constant. > > May be I should try a 10 ns coupling constant, just to see if the > simulation would go belly up. > > On Mon, Oct 13, 2014 at 11:02 AM, Michael Shirts > wrote: > >> > I guess, if I pick a coupling constant that is just small enough to >> keep the >> energy conserved, I would get a NVT simulation that is as close as a NVE >> simulation as possible. >> >> > Is this correct? >> >> Yes, but then at that point the thermostat isn't actually thermostatting. >> The Bussi comment is merely to show that his thermostat correctly reduces >> to Newton's law in the limit, not that it would be useful to run it in >> that >> limit. >> >> On Mon, Oct 13, 2014 at 10:28 AM, Johnny Lu >> wrote: >> >> > On page 014101-3, the Bussi paper (http://dx.doi.org/10.1063/1.2408420) >> > mentioned: "On the other hand, for coupling constant approaching >> > infinity,the Hamiltonian dynamics is recovered." >> > Does that means that for a large enough coupling constant, the >> velocities >> > are nearly not rescaled, and the dynamics (like rate of motion) would be >> > same as that of NVE? >> > >> > A larger coupling constant, means a smaller diffusion coefficient in the >> > axillary dynamics by equation 6. >> > >> > While the effects of the velocity rescaling at each step will >> accumulate, a >> > larger coupling constant means the thermostat perturb less of the >> dynamics, >> > and the resulting dynamics is closer to a NVE simulation. >> > There is no worry that the thermostat would suddenly rescale the >> dynamics >> > every x step, because in the procedure of the thermostat, the velocities >> > are rescaled every step, regardless of the coupling constant. >> > >> > I guess, if I pick a coupling constant that is just small enough to keep >> > the energy conserved, I would get a NVT simulation that is as close as a >> > NVE simulation as possible. >> > >> > Is this correct? >> > -- >> > 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] Use NVT to mimic NVE
I just want something that will patch up the energy lost due to numerical error of NVE simulation of the system ran by mixed precision gromacs, instead of a thermostat. I hope the velocity rescaling is sufficiently uncorrelated with the motion of the protein. So far, the simulations ran 2.5 ns, and the fluctuation of total energy seems to be within 1% of total energy, with a 100ps or 1ns coupling constant. May be I should try a 10 ns coupling constant, just to see if the simulation would go belly up. On Mon, Oct 13, 2014 at 11:02 AM, Michael Shirts wrote: > > I guess, if I pick a coupling constant that is just small enough to keep > the > energy conserved, I would get a NVT simulation that is as close as a NVE > simulation as possible. > > > Is this correct? > > Yes, but then at that point the thermostat isn't actually thermostatting. > The Bussi comment is merely to show that his thermostat correctly reduces > to Newton's law in the limit, not that it would be useful to run it in that > limit. > > On Mon, Oct 13, 2014 at 10:28 AM, Johnny Lu > wrote: > > > On page 014101-3, the Bussi paper (http://dx.doi.org/10.1063/1.2408420) > > mentioned: "On the other hand, for coupling constant approaching > > infinity,the Hamiltonian dynamics is recovered." > > Does that means that for a large enough coupling constant, the velocities > > are nearly not rescaled, and the dynamics (like rate of motion) would be > > same as that of NVE? > > > > A larger coupling constant, means a smaller diffusion coefficient in the > > axillary dynamics by equation 6. > > > > While the effects of the velocity rescaling at each step will > accumulate, a > > larger coupling constant means the thermostat perturb less of the > dynamics, > > and the resulting dynamics is closer to a NVE simulation. > > There is no worry that the thermostat would suddenly rescale the dynamics > > every x step, because in the procedure of the thermostat, the velocities > > are rescaled every step, regardless of the coupling constant. > > > > I guess, if I pick a coupling constant that is just small enough to keep > > the energy conserved, I would get a NVT simulation that is as close as a > > NVE simulation as possible. > > > > Is this correct? > > -- > > 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] Use NVT to mimic NVE
> I guess, if I pick a coupling constant that is just small enough to keep the energy conserved, I would get a NVT simulation that is as close as a NVE simulation as possible. > Is this correct? Yes, but then at that point the thermostat isn't actually thermostatting. The Bussi comment is merely to show that his thermostat correctly reduces to Newton's law in the limit, not that it would be useful to run it in that limit. On Mon, Oct 13, 2014 at 10:28 AM, Johnny Lu wrote: > On page 014101-3, the Bussi paper (http://dx.doi.org/10.1063/1.2408420) > mentioned: "On the other hand, for coupling constant approaching > infinity,the Hamiltonian dynamics is recovered." > Does that means that for a large enough coupling constant, the velocities > are nearly not rescaled, and the dynamics (like rate of motion) would be > same as that of NVE? > > A larger coupling constant, means a smaller diffusion coefficient in the > axillary dynamics by equation 6. > > While the effects of the velocity rescaling at each step will accumulate, a > larger coupling constant means the thermostat perturb less of the dynamics, > and the resulting dynamics is closer to a NVE simulation. > There is no worry that the thermostat would suddenly rescale the dynamics > every x step, because in the procedure of the thermostat, the velocities > are rescaled every step, regardless of the coupling constant. > > I guess, if I pick a coupling constant that is just small enough to keep > the energy conserved, I would get a NVT simulation that is as close as a > NVE simulation as possible. > > Is this correct? > -- > 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] Use NVT to mimic NVE
On page 014101-3, the Bussi paper (http://dx.doi.org/10.1063/1.2408420) mentioned: "On the other hand, for coupling constant approaching infinity,the Hamiltonian dynamics is recovered." Does that means that for a large enough coupling constant, the velocities are nearly not rescaled, and the dynamics (like rate of motion) would be same as that of NVE? A larger coupling constant, means a smaller diffusion coefficient in the axillary dynamics by equation 6. While the effects of the velocity rescaling at each step will accumulate, a larger coupling constant means the thermostat perturb less of the dynamics, and the resulting dynamics is closer to a NVE simulation. There is no worry that the thermostat would suddenly rescale the dynamics every x step, because in the procedure of the thermostat, the velocities are rescaled every step, regardless of the coupling constant. I guess, if I pick a coupling constant that is just small enough to keep the energy conserved, I would get a NVT simulation that is as close as a NVE simulation as possible. Is this correct? -- 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] Use NVT to mimic NVE
I am not quite in the business of folding/unfolding protein. On Sun, Oct 12, 2014 at 4:07 PM, Johnny Lu wrote: > Thank you for pointing me to that paper. I took a quick look of it > yesterday. > Would the results in the paper stay the same, if the side chain rotations > of a protein is investigated? > > On Sun, Oct 12, 2014 at 3:30 PM, Michael Shirts > wrote: > >> > If we use thermostats, the thermostats will correct the energy >> drop/raise >> caused by numerical error (which acts as a fluctuating source/sink that >> may >> not even follow the normal distribution), without causing additional >> artifacts. >> >> Thermostats correct SOME of the artifacts. It is not always clear which >> ones. >> >> > Regardless, thermostats causes artifacts, especially in dynamics and >> rates. >> >> In SOME cases it may be negligible. In others, not. It is very hard to >> say. >> >> See our paper linked before http://pubs.acs.org/doi/abs/10.1021/ct400109a >> "Effects of Temperature Control Algorithms on Transport Properties and >> Kinetics in Molecular Dynamics Simulations" which covers most short-time >> scale effects. >> >> Whether the thermostats that do not affect short time scale properties to >> any noticable degree still affect long-time scale properties through some >> sort of error accumulation is not known, nor which properties they might >> affect. >> >> >> On Sun, Oct 12, 2014 at 3:07 PM, Johnny Lu >> wrote: >> >> > oh, i still mix up things. the numerical error might act as dissipation. >> > >> > On Sun, Oct 12, 2014 at 3:01 PM, Johnny Lu >> wrote: >> > >> > > Sorry that I misunderstood your post. >> > > >> > > Can compensating energy lost caused by numerical error with thermostat >> > > cause error in the probability distribution of thermodynamic variables >> > and >> > > distribution of conformations? >> > > >> > > Below is just a guess. I don't understand the fluctuation dissipation >> > > theorem enough at this point. >> > > >> > > I would guess so.. unless the fluctuation of the velocity of the atom >> > > doesn't follow maxwell-Boltzmann distribution (I guess that can happen >> > in a >> > > crystal made of harmonic oscillator of a single frequency, or if some >> > part >> > > of the protein has low degree of freedom. This is a flaw found in >> > > nose-hover thermostats.) >> > > >> > > Otherwise, some thermostats already try to provide the correct >> > > fluctuation, so that the distribution of thermodynamic variables is >> > correct >> > > (as in fluctuation-dissipation theorem). If we use thermostats, the >> > > thermostats will correct the energy drop/raise caused by numerical >> error >> > > (which acts as a fluctuating source/sink that may not even follow the >> > > normal distribution), without causing additional artifacts. >> > > >> > > Regardless, thermostats causes artifacts, especially in dynamics and >> > rates. >> > > >> > > On Sun, Oct 12, 2014 at 2:07 PM, Michael Shirts >> > > wrote: >> > > >> > >> > The point was that if the energy leaves the system, then the system >> > >> is never in equilibrium. Not vice versa, please. >> > >> >> > >> This is incorrect logic. f there are errors in the integrator, then >> > >> F=gradient of the potential is not true. If that is not true, energy >> is >> > >> not >> > >> conserved, and energy can leave or enter the system. >> > >> >> > >> >> > >> On Sun, Oct 12, 2014 at 1:58 PM, Dr. Vitaly Chaban < >> vvcha...@gmail.com> >> > >> wrote: >> > >> >> > >> > The point was that if the energy leaves the system, then the >> system is >> > >> > never in equilibrium. Not vice versa, please. >> > >> > >> > >> > >> > >> > >> > >> > Dr. Vitaly V. Chaban >> > >> > >> > >> > Виталий Витальевич ЧАБАН >> > >> > >> > >> > >> > >> > On Sun, Oct 12, 2014 at 7:20 PM, Johnny Lu > > >> > >> wrote: >> > >> > > Why non-equilibrium can cause lost of total energy in NVE >> > simulation? >> > >> > > (baring the case that the non-equilibrium causes very large >> values >> > >> that >> > >> > > causes over flow / getting out of the stable range of algorithms >> of >> > >> > > gromacs). >> > >> > > >> > >> > > A closed system should have constant energy, regardless of >> whether >> > it >> > >> is >> > >> > at >> > >> > > equilibrium. >> > >> > > >> > >> > > I guess people use the word "converge" instead of equilibrium in >> > >> > molecular >> > >> > > dynamics simulation of protein, possibly because the simulation >> may >> > >> never >> > >> > > reach equilibrium with current computing power. >> > >> > > http://pubs.rsc.org/en/content/articlepdf/2012/cp/c2cp23961b >> > >> > > >> > >> > > I may try older version of gromacs and/or not using constraint, >> > after >> > >> > > checking the bug list and performance. I had never thought about >> > that >> > >> > route. >> > >> > > >> > >> > > >> > >> > > >> > >> > -- >> > >> > Gromacs Users mailing list >> > >> > >> > >> > * Please search the archive at >> > >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List bef
Re: [gmx-users] Use NVT to mimic NVE
Thank you for pointing me to that paper. I took a quick look of it yesterday. Would the results in the paper stay the same, if the side chain rotations of a protein is investigated? On Sun, Oct 12, 2014 at 3:30 PM, Michael Shirts wrote: > > If we use thermostats, the thermostats will correct the energy drop/raise > caused by numerical error (which acts as a fluctuating source/sink that may > not even follow the normal distribution), without causing additional > artifacts. > > Thermostats correct SOME of the artifacts. It is not always clear which > ones. > > > Regardless, thermostats causes artifacts, especially in dynamics and > rates. > > In SOME cases it may be negligible. In others, not. It is very hard to > say. > > See our paper linked before http://pubs.acs.org/doi/abs/10.1021/ct400109a > "Effects of Temperature Control Algorithms on Transport Properties and > Kinetics in Molecular Dynamics Simulations" which covers most short-time > scale effects. > > Whether the thermostats that do not affect short time scale properties to > any noticable degree still affect long-time scale properties through some > sort of error accumulation is not known, nor which properties they might > affect. > > > On Sun, Oct 12, 2014 at 3:07 PM, Johnny Lu wrote: > > > oh, i still mix up things. the numerical error might act as dissipation. > > > > On Sun, Oct 12, 2014 at 3:01 PM, Johnny Lu > wrote: > > > > > Sorry that I misunderstood your post. > > > > > > Can compensating energy lost caused by numerical error with thermostat > > > cause error in the probability distribution of thermodynamic variables > > and > > > distribution of conformations? > > > > > > Below is just a guess. I don't understand the fluctuation dissipation > > > theorem enough at this point. > > > > > > I would guess so.. unless the fluctuation of the velocity of the atom > > > doesn't follow maxwell-Boltzmann distribution (I guess that can happen > > in a > > > crystal made of harmonic oscillator of a single frequency, or if some > > part > > > of the protein has low degree of freedom. This is a flaw found in > > > nose-hover thermostats.) > > > > > > Otherwise, some thermostats already try to provide the correct > > > fluctuation, so that the distribution of thermodynamic variables is > > correct > > > (as in fluctuation-dissipation theorem). If we use thermostats, the > > > thermostats will correct the energy drop/raise caused by numerical > error > > > (which acts as a fluctuating source/sink that may not even follow the > > > normal distribution), without causing additional artifacts. > > > > > > Regardless, thermostats causes artifacts, especially in dynamics and > > rates. > > > > > > On Sun, Oct 12, 2014 at 2:07 PM, Michael Shirts > > > wrote: > > > > > >> > The point was that if the energy leaves the system, then the system > > >> is never in equilibrium. Not vice versa, please. > > >> > > >> This is incorrect logic. f there are errors in the integrator, then > > >> F=gradient of the potential is not true. If that is not true, energy > is > > >> not > > >> conserved, and energy can leave or enter the system. > > >> > > >> > > >> On Sun, Oct 12, 2014 at 1:58 PM, Dr. Vitaly Chaban < > vvcha...@gmail.com> > > >> wrote: > > >> > > >> > The point was that if the energy leaves the system, then the system > is > > >> > never in equilibrium. Not vice versa, please. > > >> > > > >> > > > >> > > > >> > Dr. Vitaly V. Chaban > > >> > > > >> > Виталий Витальевич ЧАБАН > > >> > > > >> > > > >> > On Sun, Oct 12, 2014 at 7:20 PM, Johnny Lu > > >> wrote: > > >> > > Why non-equilibrium can cause lost of total energy in NVE > > simulation? > > >> > > (baring the case that the non-equilibrium causes very large values > > >> that > > >> > > causes over flow / getting out of the stable range of algorithms > of > > >> > > gromacs). > > >> > > > > >> > > A closed system should have constant energy, regardless of whether > > it > > >> is > > >> > at > > >> > > equilibrium. > > >> > > > > >> > > I guess people use the word "converge" instead of equilibrium in > > >> > molecular > > >> > > dynamics simulation of protein, possibly because the simulation > may > > >> never > > >> > > reach equilibrium with current computing power. > > >> > > http://pubs.rsc.org/en/content/articlepdf/2012/cp/c2cp23961b > > >> > > > > >> > > I may try older version of gromacs and/or not using constraint, > > after > > >> > > checking the bug list and performance. I had never thought about > > that > > >> > route. > > >> > > > > >> > > > > >> > > > > >> > -- > > >> > 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-r
Re: [gmx-users] Use NVT to mimic NVE
> If we use thermostats, the thermostats will correct the energy drop/raise caused by numerical error (which acts as a fluctuating source/sink that may not even follow the normal distribution), without causing additional artifacts. Thermostats correct SOME of the artifacts. It is not always clear which ones. > Regardless, thermostats causes artifacts, especially in dynamics and rates. In SOME cases it may be negligible. In others, not. It is very hard to say. See our paper linked before http://pubs.acs.org/doi/abs/10.1021/ct400109a "Effects of Temperature Control Algorithms on Transport Properties and Kinetics in Molecular Dynamics Simulations" which covers most short-time scale effects. Whether the thermostats that do not affect short time scale properties to any noticable degree still affect long-time scale properties through some sort of error accumulation is not known, nor which properties they might affect. On Sun, Oct 12, 2014 at 3:07 PM, Johnny Lu wrote: > oh, i still mix up things. the numerical error might act as dissipation. > > On Sun, Oct 12, 2014 at 3:01 PM, Johnny Lu wrote: > > > Sorry that I misunderstood your post. > > > > Can compensating energy lost caused by numerical error with thermostat > > cause error in the probability distribution of thermodynamic variables > and > > distribution of conformations? > > > > Below is just a guess. I don't understand the fluctuation dissipation > > theorem enough at this point. > > > > I would guess so.. unless the fluctuation of the velocity of the atom > > doesn't follow maxwell-Boltzmann distribution (I guess that can happen > in a > > crystal made of harmonic oscillator of a single frequency, or if some > part > > of the protein has low degree of freedom. This is a flaw found in > > nose-hover thermostats.) > > > > Otherwise, some thermostats already try to provide the correct > > fluctuation, so that the distribution of thermodynamic variables is > correct > > (as in fluctuation-dissipation theorem). If we use thermostats, the > > thermostats will correct the energy drop/raise caused by numerical error > > (which acts as a fluctuating source/sink that may not even follow the > > normal distribution), without causing additional artifacts. > > > > Regardless, thermostats causes artifacts, especially in dynamics and > rates. > > > > On Sun, Oct 12, 2014 at 2:07 PM, Michael Shirts > > wrote: > > > >> > The point was that if the energy leaves the system, then the system > >> is never in equilibrium. Not vice versa, please. > >> > >> This is incorrect logic. f there are errors in the integrator, then > >> F=gradient of the potential is not true. If that is not true, energy is > >> not > >> conserved, and energy can leave or enter the system. > >> > >> > >> On Sun, Oct 12, 2014 at 1:58 PM, Dr. Vitaly Chaban > >> wrote: > >> > >> > The point was that if the energy leaves the system, then the system is > >> > never in equilibrium. Not vice versa, please. > >> > > >> > > >> > > >> > Dr. Vitaly V. Chaban > >> > > >> > Виталий Витальевич ЧАБАН > >> > > >> > > >> > On Sun, Oct 12, 2014 at 7:20 PM, Johnny Lu > >> wrote: > >> > > Why non-equilibrium can cause lost of total energy in NVE > simulation? > >> > > (baring the case that the non-equilibrium causes very large values > >> that > >> > > causes over flow / getting out of the stable range of algorithms of > >> > > gromacs). > >> > > > >> > > A closed system should have constant energy, regardless of whether > it > >> is > >> > at > >> > > equilibrium. > >> > > > >> > > I guess people use the word "converge" instead of equilibrium in > >> > molecular > >> > > dynamics simulation of protein, possibly because the simulation may > >> never > >> > > reach equilibrium with current computing power. > >> > > http://pubs.rsc.org/en/content/articlepdf/2012/cp/c2cp23961b > >> > > > >> > > I may try older version of gromacs and/or not using constraint, > after > >> > > checking the bug list and performance. I had never thought about > that > >> > route. > >> > > > >> > > > >> > > > >> > -- > >> > 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 >
Re: [gmx-users] Use NVT to mimic NVE
oh, i still mix up things. the numerical error might act as dissipation. On Sun, Oct 12, 2014 at 3:01 PM, Johnny Lu wrote: > Sorry that I misunderstood your post. > > Can compensating energy lost caused by numerical error with thermostat > cause error in the probability distribution of thermodynamic variables and > distribution of conformations? > > Below is just a guess. I don't understand the fluctuation dissipation > theorem enough at this point. > > I would guess so.. unless the fluctuation of the velocity of the atom > doesn't follow maxwell-Boltzmann distribution (I guess that can happen in a > crystal made of harmonic oscillator of a single frequency, or if some part > of the protein has low degree of freedom. This is a flaw found in > nose-hover thermostats.) > > Otherwise, some thermostats already try to provide the correct > fluctuation, so that the distribution of thermodynamic variables is correct > (as in fluctuation-dissipation theorem). If we use thermostats, the > thermostats will correct the energy drop/raise caused by numerical error > (which acts as a fluctuating source/sink that may not even follow the > normal distribution), without causing additional artifacts. > > Regardless, thermostats causes artifacts, especially in dynamics and rates. > > On Sun, Oct 12, 2014 at 2:07 PM, Michael Shirts > wrote: > >> > The point was that if the energy leaves the system, then the system >> is never in equilibrium. Not vice versa, please. >> >> This is incorrect logic. f there are errors in the integrator, then >> F=gradient of the potential is not true. If that is not true, energy is >> not >> conserved, and energy can leave or enter the system. >> >> >> On Sun, Oct 12, 2014 at 1:58 PM, Dr. Vitaly Chaban >> wrote: >> >> > The point was that if the energy leaves the system, then the system is >> > never in equilibrium. Not vice versa, please. >> > >> > >> > >> > Dr. Vitaly V. Chaban >> > >> > Виталий Витальевич ЧАБАН >> > >> > >> > On Sun, Oct 12, 2014 at 7:20 PM, Johnny Lu >> wrote: >> > > Why non-equilibrium can cause lost of total energy in NVE simulation? >> > > (baring the case that the non-equilibrium causes very large values >> that >> > > causes over flow / getting out of the stable range of algorithms of >> > > gromacs). >> > > >> > > A closed system should have constant energy, regardless of whether it >> is >> > at >> > > equilibrium. >> > > >> > > I guess people use the word "converge" instead of equilibrium in >> > molecular >> > > dynamics simulation of protein, possibly because the simulation may >> never >> > > reach equilibrium with current computing power. >> > > http://pubs.rsc.org/en/content/articlepdf/2012/cp/c2cp23961b >> > > >> > > I may try older version of gromacs and/or not using constraint, after >> > > checking the bug list and performance. I had never thought about that >> > route. >> > > >> > > >> > > >> > -- >> > 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] Use NVT to mimic NVE
Sorry that I misunderstood your post. Can compensating energy lost caused by numerical error with thermostat cause error in the probability distribution of thermodynamic variables and distribution of conformations? Below is just a guess. I don't understand the fluctuation dissipation theorem enough at this point. I would guess so.. unless the fluctuation of the velocity of the atom doesn't follow maxwell-Boltzmann distribution (I guess that can happen in a crystal made of harmonic oscillator of a single frequency, or if some part of the protein has low degree of freedom. This is a flaw found in nose-hover thermostats.) Otherwise, some thermostats already try to provide the correct fluctuation, so that the distribution of thermodynamic variables is correct (as in fluctuation-dissipation theorem). If we use thermostats, the thermostats will correct the energy drop/raise caused by numerical error (which acts as a fluctuating source/sink that may not even follow the normal distribution), without causing additional artifacts. Regardless, thermostats causes artifacts, especially in dynamics and rates. On Sun, Oct 12, 2014 at 2:07 PM, Michael Shirts wrote: > > The point was that if the energy leaves the system, then the system > is never in equilibrium. Not vice versa, please. > > This is incorrect logic. f there are errors in the integrator, then > F=gradient of the potential is not true. If that is not true, energy is not > conserved, and energy can leave or enter the system. > > > On Sun, Oct 12, 2014 at 1:58 PM, Dr. Vitaly Chaban > wrote: > > > The point was that if the energy leaves the system, then the system is > > never in equilibrium. Not vice versa, please. > > > > > > > > Dr. Vitaly V. Chaban > > > > Виталий Витальевич ЧАБАН > > > > > > On Sun, Oct 12, 2014 at 7:20 PM, Johnny Lu > wrote: > > > Why non-equilibrium can cause lost of total energy in NVE simulation? > > > (baring the case that the non-equilibrium causes very large values that > > > causes over flow / getting out of the stable range of algorithms of > > > gromacs). > > > > > > A closed system should have constant energy, regardless of whether it > is > > at > > > equilibrium. > > > > > > I guess people use the word "converge" instead of equilibrium in > > molecular > > > dynamics simulation of protein, possibly because the simulation may > never > > > reach equilibrium with current computing power. > > > http://pubs.rsc.org/en/content/articlepdf/2012/cp/c2cp23961b > > > > > > I may try older version of gromacs and/or not using constraint, after > > > checking the bug list and performance. I had never thought about that > > route. > > > > > > > > > > > -- > > 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] Use NVT to mimic NVE
> The point was that if the energy leaves the system, then the system is never in equilibrium. Not vice versa, please. This is incorrect logic. f there are errors in the integrator, then F=gradient of the potential is not true. If that is not true, energy is not conserved, and energy can leave or enter the system. On Sun, Oct 12, 2014 at 1:58 PM, Dr. Vitaly Chaban wrote: > The point was that if the energy leaves the system, then the system is > never in equilibrium. Not vice versa, please. > > > > Dr. Vitaly V. Chaban > > Виталий Витальевич ЧАБАН > > > On Sun, Oct 12, 2014 at 7:20 PM, Johnny Lu wrote: > > Why non-equilibrium can cause lost of total energy in NVE simulation? > > (baring the case that the non-equilibrium causes very large values that > > causes over flow / getting out of the stable range of algorithms of > > gromacs). > > > > A closed system should have constant energy, regardless of whether it is > at > > equilibrium. > > > > I guess people use the word "converge" instead of equilibrium in > molecular > > dynamics simulation of protein, possibly because the simulation may never > > reach equilibrium with current computing power. > > http://pubs.rsc.org/en/content/articlepdf/2012/cp/c2cp23961b > > > > I may try older version of gromacs and/or not using constraint, after > > checking the bug list and performance. I had never thought about that > route. > > > > > > > -- > 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] Use NVT to mimic NVE
The point was that if the energy leaves the system, then the system is never in equilibrium. Not vice versa, please. Dr. Vitaly V. Chaban Виталий Витальевич ЧАБАН On Sun, Oct 12, 2014 at 7:20 PM, Johnny Lu wrote: > Why non-equilibrium can cause lost of total energy in NVE simulation? > (baring the case that the non-equilibrium causes very large values that > causes over flow / getting out of the stable range of algorithms of > gromacs). > > A closed system should have constant energy, regardless of whether it is at > equilibrium. > > I guess people use the word "converge" instead of equilibrium in molecular > dynamics simulation of protein, possibly because the simulation may never > reach equilibrium with current computing power. > http://pubs.rsc.org/en/content/articlepdf/2012/cp/c2cp23961b > > I may try older version of gromacs and/or not using constraint, after > checking the bug list and performance. I had never thought about that route. > > > -- 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] Use NVT to mimic NVE
On 2014-10-12 17:31, Dr. Vitaly Chaban wrote: The artifacts are caused by energy leakage. Thermostatting does not solve them. The problem exists, but you do not see it clearly with thermostat. For instance, I have an example where a liquid droplet in vacuum is not stable due to bad energy conservation. Some particles just sporadically fly away over the course of the simulation. We have run 3 microsecond simulations of water droplets in vacuum with perfect energy conservation, double precision, no cut-off and SETTLE. With constraint solvers it is indeed close to impossible to get real energy conservation. Turning off the constraints and using a time step <= 0.5 fs might work somewhat better with mixed precision, and these degrees of freedom may be important for energy transfer too. NVE generally does not like constraints. If I remember correctly from the previous messages, you use constraints. Novel performance improvements in gromacs (accumulated after 4.0 and especially after 4.5) sometimes compromise accuracy, though it is a long discussion itself. What about downgrading to gmx 4.0 or gmx 3.3, after all? The very last time I used gromacs for NVE simulation was in 2009. I guess I used gmx 3.3.3 (but maybe 4.0.x). There were no problems for sure. I would also give a try to some very simple system (e.g. liquid argon) to observe what happens to total energy. Good luck with troubleshooting! Dr. Vitaly V. Chaban Виталий Витальевич ЧАБАН On Sun, Oct 12, 2014 at 4:53 PM, Johnny Lu wrote: Firstly, what are the possible errors/artifacts caused by masking "the energy leakage problem with the thermostat" in this case? Secondly, are there any other mdp setting that I can try to make the mixed precision gromacs NVE run have conserved energy over 100 ns ? (and... is it because of some errors that I made in my systems that make the NVE run not conserved in energy?) The NVE has the following statistics. Statistics over 2747281 steps [ 0. through 1373.6400 ps ], 4 data sets All statistics are over 274729 points Energy Average Err.Est. RMSD Tot-Drift --- Disper. corr. -3961.13 0 0 2.60178e-09 (kJ/mol) Total Energy-309939160 337.76478.828 (kJ/mol) Temperature 300.292 0.241.49289 0.631428 (K) Pressure -64.54094.7148.77925.1326 (bar) -- 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. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] Use NVT to mimic NVE
Why non-equilibrium can cause lost of total energy in NVE simulation? (baring the case that the non-equilibrium causes very large values that causes over flow / getting out of the stable range of algorithms of gromacs). A closed system should have constant energy, regardless of whether it is at equilibrium. I guess people use the word "converge" instead of equilibrium in molecular dynamics simulation of protein, possibly because the simulation may never reach equilibrium with current computing power. http://pubs.rsc.org/en/content/articlepdf/2012/cp/c2cp23961b I may try older version of gromacs and/or not using constraint, after checking the bug list and performance. I had never thought about that route. -- 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] Use NVT to mimic NVE
I believe the major problem with energy losses is that your system never achieves equilibrium. Thus, all the simulated properties are not what they need to be... Dr. Vitaly V. Chaban Виталий Витальевич ЧАБАН On Sun, Oct 12, 2014 at 5:31 PM, Dr. Vitaly Chaban wrote: > The artifacts are caused by energy leakage. Thermostatting does not > solve them. The problem exists, but you do not see it clearly with > thermostat. For instance, I have an example where a liquid droplet in > vacuum is not stable due to bad energy conservation. Some particles > just sporadically fly away over the course of the simulation. > > NVE generally does not like constraints. If I remember correctly from > the previous messages, you use constraints. Novel performance > improvements in gromacs (accumulated after 4.0 and especially after > 4.5) sometimes compromise accuracy, though it is a long discussion > itself. What about downgrading to gmx 4.0 or gmx 3.3, after all? The > very last time I used gromacs for NVE simulation was in 2009. I guess > I used gmx 3.3.3 (but maybe 4.0.x). There were no problems for sure. > > I would also give a try to some very simple system (e.g. liquid argon) > to observe what happens to total energy. > > Good luck with troubleshooting! > > > Dr. Vitaly V. Chaban > > Виталий Витальевич ЧАБАН > > > On Sun, Oct 12, 2014 at 4:53 PM, Johnny Lu wrote: >> Firstly, what are the possible errors/artifacts caused by masking "the >> energy leakage problem with the thermostat" in this case? >> >> Secondly, are there any other mdp setting that I can try to make the mixed >> precision gromacs NVE run have conserved energy over 100 ns ? (and... is it >> because of some errors that I made in my systems that make the NVE run not >> conserved in energy?) >> >> The NVE has the following statistics. >> >> Statistics over 2747281 steps [ 0. through 1373.6400 ps ], 4 data sets >> All statistics are over 274729 points >> >> Energy Average Err.Est. RMSD Tot-Drift >> --- >> Disper. corr. -3961.13 0 0 2.60178e-09 >> (kJ/mol) >> Total Energy-309939160 337.76478.828 >> (kJ/mol) >> Temperature 300.292 0.241.49289 0.631428 (K) >> Pressure -64.54094.7148.77925.1326 (bar) >> -- >> 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] Use NVT to mimic NVE
The artifacts are caused by energy leakage. Thermostatting does not solve them. The problem exists, but you do not see it clearly with thermostat. For instance, I have an example where a liquid droplet in vacuum is not stable due to bad energy conservation. Some particles just sporadically fly away over the course of the simulation. NVE generally does not like constraints. If I remember correctly from the previous messages, you use constraints. Novel performance improvements in gromacs (accumulated after 4.0 and especially after 4.5) sometimes compromise accuracy, though it is a long discussion itself. What about downgrading to gmx 4.0 or gmx 3.3, after all? The very last time I used gromacs for NVE simulation was in 2009. I guess I used gmx 3.3.3 (but maybe 4.0.x). There were no problems for sure. I would also give a try to some very simple system (e.g. liquid argon) to observe what happens to total energy. Good luck with troubleshooting! Dr. Vitaly V. Chaban Виталий Витальевич ЧАБАН On Sun, Oct 12, 2014 at 4:53 PM, Johnny Lu wrote: > Firstly, what are the possible errors/artifacts caused by masking "the > energy leakage problem with the thermostat" in this case? > > Secondly, are there any other mdp setting that I can try to make the mixed > precision gromacs NVE run have conserved energy over 100 ns ? (and... is it > because of some errors that I made in my systems that make the NVE run not > conserved in energy?) > > The NVE has the following statistics. > > Statistics over 2747281 steps [ 0. through 1373.6400 ps ], 4 data sets > All statistics are over 274729 points > > Energy Average Err.Est. RMSD Tot-Drift > --- > Disper. corr. -3961.13 0 0 2.60178e-09 > (kJ/mol) > Total Energy-309939160 337.76478.828 > (kJ/mol) > Temperature 300.292 0.241.49289 0.631428 (K) > Pressure -64.54094.7148.77925.1326 (bar) > -- > 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] Use NVT to mimic NVE
Firstly, what are the possible errors/artifacts caused by masking "the energy leakage problem with the thermostat" in this case? Secondly, are there any other mdp setting that I can try to make the mixed precision gromacs NVE run have conserved energy over 100 ns ? (and... is it because of some errors that I made in my systems that make the NVE run not conserved in energy?) The NVE has the following statistics. Statistics over 2747281 steps [ 0. through 1373.6400 ps ], 4 data sets All statistics are over 274729 points Energy Average Err.Est. RMSD Tot-Drift --- Disper. corr. -3961.13 0 0 2.60178e-09 (kJ/mol) Total Energy-309939160 337.76478.828 (kJ/mol) Temperature 300.292 0.241.49289 0.631428 (K) Pressure -64.54094.7148.77925.1326 (bar) -- 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] Use NVT to mimic NVE
Thus, what is your question now? :-) The total energy must remain conserved at all times. That's it. Dr. Vitaly V. Chaban Виталий Витальевич ЧАБАН On Sun, Oct 12, 2014 at 2:45 AM, Johnny Lu wrote: > I tried PME and then potential-shift-verlet for Van der Waals. The energy > is still not constant in mixed precision gromacs 5.0.1 NVE run on 12 xeon > cpu without gpu. Those were nearly the last few things that I knew that I > can try in mixed precision. The system has ~165 amino acid, ~9000 water, > and 3 Cl- ion in a truncated rhombic dodecahedron box. Total energy of the > following simulation drift constantly down. This production run was a > continuation of ~300ns npt and ~300ns nvt. The PME grid was 80x80x80. > > ; Run parameters > integrator = md-vv ; leap-frog integrator > nsteps = 15000 ; 1 ns > dt = 0.0005; 0.5 fs > > ;NVE > ; nstcomm = 500 ; remove center of mass motion to reduce energy and > temp. drift. (seems less drift without this) > shake-tol = 0.01 ; shake tolerance. > verlet-buffer-tolerance = 0.0005 > > ;Output control > nstenergy = 20 ; save energies every 1.0 ps > > nstlog = 100 ; update log file every 0.2 ps > ; Bond parameters > continuation= yes ; Restarting after NVT > constraint_algorithm = lincs; holonomic constraints > constraints = all-bonds ; all bonds (even heavy atom-H bonds) > constrained > lincs_iter = 2 ; accuracy of LINCS > lincs_order = 4 ; also related to accuracy > ; Neighborsearching > ns_type = grid ; search neighboring grid cells > nstlist = 5 ; 10 fs > > vdw-modifier = Potential-shift-Verlet; > > rlist = 1.1 ; short-range neighborlist cutoff (in nm) > rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) > rvdw= 1.0 ; short-range van der Waals cutoff (in nm) > ; Electrostatics > coulombtype = PME ; Particle Mesh Ewald for long-range > electrostatics > pme_order = 6 ; cubic interpolation > fourierspacing = 0.1 ; grid spacing for FFT > > ; Temperature coupling is off > tcoupl = no; modified Berendsen thermostat > ; Pressure coupling is off > pcoupl = no > > refcoord_scaling = com > ; Periodic boundary conditions > pbc = xyz ; 3-D PBC > ; Dispersion correction > DispCorr= EnerPres ; account for cut-off vdW scheme > ; Velocity generation > gen_vel = no; Velocity generation is off > cutoff-scheme = Verlet > > > I guess the energy leakage when no thermostat is used doesn't mean the > distribution of conformation is incorrect when a thermostat is used. > Since double precision run is stable while single precision is not, the > energy leakage is caused by numerical error of the computer operation and > algorithm instead of the physics or conformation of the setup. (only the > precision changed. the mdp files were the same.) > > I also guess that the majority of simulations in published paper would have > such constant drop/rise of total energy if the thermostat is switched off. > ( Is this true??? ) > > When the Amber99ff-ILDN force field is made, NPT and NVT is used, instead > of NVE [http://dx.doi.org/10.1002%2Fprot.22711] > > The Amber lipid 14 forcefield uses NPT to create the parameters. In one of > the validations, they ran NPT followed by NVE to calculate diffusion > coefficient. The tolerance was more stringent in the NVE part than the NPT > part. The plot of energy v.s. time seems to be not in the paper. [ > http://pubs.acs.org/doi/full/10.1021/ct4010307] > > Dynamics is another matter. Langevin thermostats removes momentum transfer > and changes the rate dynamics, despite it samples the canonical ensemble > ... if the system is ergodic in practice. Two different simulations can > converge, if the string of random numbers used in langevin thermostats is > the same. I'm not sure about V-rescaling. > > I agree that all thermostats and barostats likely cause some artifacts in > dynamics. > > > On Sat, Oct 11, 2014 at 5:29 PM, Dr. Vitaly Chaban > wrote: > >> Well, if it does not conserve total energy, than such a computational >> experiment is not reliable. This is a sad truth. >> >> Philosophically, you have two options here. Either you accept that >> energy leakage is significant and then you must fight against it >> (smaller time-step, double precision, constraints, etc), or -- on the >> contrary -- you say that energy loss can be neglected and proceed "as >> is". >> >> My personal rule is if the system does not lose more than 2% of total >> energy during an entire run, the result is acceptable. I can be >> criticized for this voluntary assumption, obviously. >> >> Anyway, tricks with T-coupling constitute a very bad idea in this >> case. You basically try to mask the ene
Re: [gmx-users] Use NVT to mimic NVE
I tried PME and then potential-shift-verlet for Van der Waals. The energy is still not constant in mixed precision gromacs 5.0.1 NVE run on 12 xeon cpu without gpu. Those were nearly the last few things that I knew that I can try in mixed precision. The system has ~165 amino acid, ~9000 water, and 3 Cl- ion in a truncated rhombic dodecahedron box. Total energy of the following simulation drift constantly down. This production run was a continuation of ~300ns npt and ~300ns nvt. The PME grid was 80x80x80. ; Run parameters integrator = md-vv ; leap-frog integrator nsteps = 15000 ; 1 ns dt = 0.0005; 0.5 fs ;NVE ; nstcomm = 500 ; remove center of mass motion to reduce energy and temp. drift. (seems less drift without this) shake-tol = 0.01 ; shake tolerance. verlet-buffer-tolerance = 0.0005 ;Output control nstenergy = 20 ; save energies every 1.0 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation= yes ; Restarting after NVT constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 2 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs vdw-modifier = Potential-shift-Verlet; rlist = 1.1 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 6 ; cubic interpolation fourierspacing = 0.1 ; grid spacing for FFT ; Temperature coupling is off tcoupl = no; modified Berendsen thermostat ; Pressure coupling is off pcoupl = no refcoord_scaling = com ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no; Velocity generation is off cutoff-scheme = Verlet I guess the energy leakage when no thermostat is used doesn't mean the distribution of conformation is incorrect when a thermostat is used. Since double precision run is stable while single precision is not, the energy leakage is caused by numerical error of the computer operation and algorithm instead of the physics or conformation of the setup. (only the precision changed. the mdp files were the same.) I also guess that the majority of simulations in published paper would have such constant drop/rise of total energy if the thermostat is switched off. ( Is this true??? ) When the Amber99ff-ILDN force field is made, NPT and NVT is used, instead of NVE [http://dx.doi.org/10.1002%2Fprot.22711] The Amber lipid 14 forcefield uses NPT to create the parameters. In one of the validations, they ran NPT followed by NVE to calculate diffusion coefficient. The tolerance was more stringent in the NVE part than the NPT part. The plot of energy v.s. time seems to be not in the paper. [ http://pubs.acs.org/doi/full/10.1021/ct4010307] Dynamics is another matter. Langevin thermostats removes momentum transfer and changes the rate dynamics, despite it samples the canonical ensemble ... if the system is ergodic in practice. Two different simulations can converge, if the string of random numbers used in langevin thermostats is the same. I'm not sure about V-rescaling. I agree that all thermostats and barostats likely cause some artifacts in dynamics. On Sat, Oct 11, 2014 at 5:29 PM, Dr. Vitaly Chaban wrote: > Well, if it does not conserve total energy, than such a computational > experiment is not reliable. This is a sad truth. > > Philosophically, you have two options here. Either you accept that > energy leakage is significant and then you must fight against it > (smaller time-step, double precision, constraints, etc), or -- on the > contrary -- you say that energy loss can be neglected and proceed "as > is". > > My personal rule is if the system does not lose more than 2% of total > energy during an entire run, the result is acceptable. I can be > criticized for this voluntary assumption, obviously. > > Anyway, tricks with T-coupling constitute a very bad idea in this > case. You basically try to mask the energy leakage problem with the > thermostat. Thermostat never removes the problem itself. > > > Dr. Vitaly V. Chaban > > Виталий Витальевич ЧАБАН > > > On Sat, Oct 11, 2014 at 11:12 PM, Johnny Lu > wrote: > > I tried NVE on single precision gromacs 4.6.7 with and without GPU. > > The energy either drift down or up, depending on the mdp file, and the > drift > > seems linear. > > > > Linear
Re: [gmx-users] Use NVT to mimic NVE
Well, if it does not conserve total energy, than such a computational experiment is not reliable. This is a sad truth. Philosophically, you have two options here. Either you accept that energy leakage is significant and then you must fight against it (smaller time-step, double precision, constraints, etc), or -- on the contrary -- you say that energy loss can be neglected and proceed "as is". My personal rule is if the system does not lose more than 2% of total energy during an entire run, the result is acceptable. I can be criticized for this voluntary assumption, obviously. Anyway, tricks with T-coupling constitute a very bad idea in this case. You basically try to mask the energy leakage problem with the thermostat. Thermostat never removes the problem itself. Dr. Vitaly V. Chaban Виталий Витальевич ЧАБАН On Sat, Oct 11, 2014 at 11:12 PM, Johnny Lu wrote: > I tried NVE on single precision gromacs 4.6.7 with and without GPU. > The energy either drift down or up, depending on the mdp file, and the drift > seems linear. > > Linear fit says that if I run 100 ns simulation, at the end the energy is > doubled. > > If I use double precision gromacs, the drift seems insignificant over 100 ns > simulation by linear regression fitting on a 300 ps run. > But double precision gromacs can't use gpu and is much slower than single > precision gromacs. > > On Sat, Oct 11, 2014 at 4:33 PM, Dr. Vitaly Chaban > wrote: >> >> I also cannot get why not to just turn off the thermostat... >> >> If energy transfer phenomena are in focus, NVE is an ensemble of >> choice, no matter which relaxation constant is used for the T-coupling >> algorithm. >> >> >> Dr. Vitaly V. Chaban >> >> Виталий Витальевич ЧАБАН >> >> >> On Sat, Oct 11, 2014 at 6:32 PM, Antonio Baptista >> wrote: >> > Then, run true NVE, for the reasons we already pointed. >> > >> > On Sat, 11 Oct 2014, Johnny Lu wrote: >> > >> >> For dynamics with correct rate and correct fluctuation. >> >> >> >> On Sat, Oct 11, 2014 at 8:09 AM, Dr. Vitaly Chaban >> >> wrote: >> >> >> >>> what is it needed for? >> >>> >> >>> >> >>> >> >>> Dr. Vitaly V. Chaban >> >>> >> >>> Виталий Витальевич ЧАБАН >> >>> >> >>> >> >>> On Fri, Oct 10, 2014 at 7:41 PM, Johnny Lu >> >>> wrote: >> >>> > Hi. >> >>> > >> >>> > Is it a good idea to mimic NVE by a NVT simulation with a large >> >>> temperature >> >>> > coupling time constant, to reduce the effect of the thermostat ? >> >>> > >> >>> > If I use V-rescale thermostat, what artifacts will the simulation >> >>> > get >> >>> > if >> >>> I >> >>> > use a large coupling time (say, 500 ps) and single precision gromacs >> >>> > ? >> >>> > >> >>> > 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. > > -- 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://ww
Re: [gmx-users] Use NVT to mimic NVE
I tried NVE on single precision gromacs 4.6.7 with and without GPU. The energy either drift down or up, depending on the mdp file, and the drift seems linear. Linear fit says that if I run 100 ns simulation, at the end the energy is doubled. If I use double precision gromacs, the drift seems insignificant over 100 ns simulation by linear regression fitting on a 300 ps run. But double precision gromacs can't use gpu and is much slower than single precision gromacs. On Sat, Oct 11, 2014 at 4:33 PM, Dr. Vitaly Chaban wrote: > I also cannot get why not to just turn off the thermostat... > > If energy transfer phenomena are in focus, NVE is an ensemble of > choice, no matter which relaxation constant is used for the T-coupling > algorithm. > > > Dr. Vitaly V. Chaban > > Виталий Витальевич ЧАБАН > > > On Sat, Oct 11, 2014 at 6:32 PM, Antonio Baptista > wrote: > > Then, run true NVE, for the reasons we already pointed. > > > > On Sat, 11 Oct 2014, Johnny Lu wrote: > > > >> For dynamics with correct rate and correct fluctuation. > >> > >> On Sat, Oct 11, 2014 at 8:09 AM, Dr. Vitaly Chaban > >> wrote: > >> > >>> what is it needed for? > >>> > >>> > >>> > >>> Dr. Vitaly V. Chaban > >>> > >>> Виталий Витальевич ЧАБАН > >>> > >>> > >>> On Fri, Oct 10, 2014 at 7:41 PM, Johnny Lu > >>> wrote: > >>> > Hi. > >>> > > >>> > Is it a good idea to mimic NVE by a NVT simulation with a large > >>> temperature > >>> > coupling time constant, to reduce the effect of the thermostat ? > >>> > > >>> > If I use V-rescale thermostat, what artifacts will the simulation get > >>> > if > >>> I > >>> > use a large coupling time (say, 500 ps) and single precision gromacs > ? > >>> > > >>> > 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. > -- 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] Use NVT to mimic NVE
I also cannot get why not to just turn off the thermostat... If energy transfer phenomena are in focus, NVE is an ensemble of choice, no matter which relaxation constant is used for the T-coupling algorithm. Dr. Vitaly V. Chaban Виталий Витальевич ЧАБАН On Sat, Oct 11, 2014 at 6:32 PM, Antonio Baptista wrote: > Then, run true NVE, for the reasons we already pointed. > > On Sat, 11 Oct 2014, Johnny Lu wrote: > >> For dynamics with correct rate and correct fluctuation. >> >> On Sat, Oct 11, 2014 at 8:09 AM, Dr. Vitaly Chaban >> wrote: >> >>> what is it needed for? >>> >>> >>> >>> Dr. Vitaly V. Chaban >>> >>> Виталий Витальевич ЧАБАН >>> >>> >>> On Fri, Oct 10, 2014 at 7:41 PM, Johnny Lu >>> wrote: >>> > Hi. >>> > >>> > Is it a good idea to mimic NVE by a NVT simulation with a large >>> temperature >>> > coupling time constant, to reduce the effect of the thermostat ? >>> > >>> > If I use V-rescale thermostat, what artifacts will the simulation get >>> > if >>> I >>> > use a large coupling time (say, 500 ps) and single precision gromacs ? >>> > >>> > 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.
Re: [gmx-users] Use NVT to mimic NVE
Then, run true NVE, for the reasons we already pointed. On Sat, 11 Oct 2014, Johnny Lu wrote: For dynamics with correct rate and correct fluctuation. On Sat, Oct 11, 2014 at 8:09 AM, Dr. Vitaly Chaban wrote: what is it needed for? Dr. Vitaly V. Chaban Виталий Витальевич ЧАБАН On Fri, Oct 10, 2014 at 7:41 PM, Johnny Lu wrote: > Hi. > > Is it a good idea to mimic NVE by a NVT simulation with a large temperature > coupling time constant, to reduce the effect of the thermostat ? > > If I use V-rescale thermostat, what artifacts will the simulation get if I > use a large coupling time (say, 500 ps) and single precision gromacs ? > > 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] Use NVT to mimic NVE
For dynamics with correct rate and correct fluctuation. On Sat, Oct 11, 2014 at 8:09 AM, Dr. Vitaly Chaban wrote: > what is it needed for? > > > > Dr. Vitaly V. Chaban > > Виталий Витальевич ЧАБАН > > > On Fri, Oct 10, 2014 at 7:41 PM, Johnny Lu wrote: > > Hi. > > > > Is it a good idea to mimic NVE by a NVT simulation with a large > temperature > > coupling time constant, to reduce the effect of the thermostat ? > > > > If I use V-rescale thermostat, what artifacts will the simulation get if > I > > use a large coupling time (say, 500 ps) and single precision gromacs ? > > > > 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] Use NVT to mimic NVE
Following up on fluctuations and ensembles: The following paper discusses tests of whether an ensemble has the correct distribution of energies, including fluctuations of all scale: "Simple quantitative tests to validate sampling from thermodynamic ensembles" http://pubs.acs.org/doi/abs/10.1021/ct300688p Turns out that v-rescale behaves very well, at least for fluctuations of the total energy. In the limit of large scale, for NVE and NVT (if carried out at the temperature where _NVT = E_NVE, then all system averages (including pressure, etc) will be equal. But the fluctuations (which include 2nd derivative properties like heat capacity, etc). will not be equal. So it depends on what you are interested in. If you are interested in thermodynamics, just go ahead and run the ensemble you are interested in. If you are interested in dynamics, you can check out this paper which partly answers the questions of what the artifacts are created by thermostats. Again, vrescale is quite good -- Langevin or anything with stochastic noise is not so good. "Effects of Temperature Control Algorithms on Transport Properties and Kinetics in Molecular Dynamics Simulations" http://pubs.acs.org/doi/abs/10.1021/ct400109a Best, Michael Shirts Associate Professor Department of Chemical Engineering University of Virginia michael.shi...@virginia.edu (434)-243-1821 On Fri, Oct 10, 2014 at 7:40 PM, Antonio Baptista wrote: > On Fri, 10 Oct 2014, Mark Abraham wrote: > > On Fri, Oct 10, 2014 at 7:41 PM, Johnny Lu >> wrote: >> >> Hi. >>> >>> Is it a good idea to mimic NVE by a NVT simulation with a large >>> temperature >>> coupling time constant, to reduce the effect of the thermostat ? >>> >>> >> Not if your observable is the total energy. But for most interesting >> observables, this is more than fine. >> >> >> If I use V-rescale thermostat, what artifacts will the simulation get if >>> I >>> use a large coupling time (say, 500 ps) and single precision gromacs ? >>> >>> >> Probably nobody knows :-) Thermodynamic ensemble differences disappear as >> the system becomes large. But quantifying that from converged ensembles >> for >> a given observable is work. >> >> Mark >> > > Note also that, unlike averages, fluctuations are ensemble-dependent. > Although v-rescaling (as most other thermostats) does indeed sample from > the NVE ensemble in the mathematical limit of infinite coupling constant, > this does not imply that, in practice, fluctuations converge to those in > the NVE ensemble for large but finite coupling constants. > > As you can check in the v-rescaling paper, fluctuations were found to be > very robust to changes of the coupling parameter (at least for the kinetic > and potential energies). This is generally a good thing, but maybe not what > you want to run a "fake" NVE simulation as you described. So, if you are > interested in the fluctuations of some properties, you will have to check > what is in practice their asymptotic behavior. > > Best, > Antonio > > > > >> >> 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] Use NVT to mimic NVE
what is it needed for? Dr. Vitaly V. Chaban Виталий Витальевич ЧАБАН On Fri, Oct 10, 2014 at 7:41 PM, Johnny Lu wrote: > Hi. > > Is it a good idea to mimic NVE by a NVT simulation with a large temperature > coupling time constant, to reduce the effect of the thermostat ? > > If I use V-rescale thermostat, what artifacts will the simulation get if I > use a large coupling time (say, 500 ps) and single precision gromacs ? > > 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] Use NVT to mimic NVE
On Fri, 10 Oct 2014, Mark Abraham wrote: On Fri, Oct 10, 2014 at 7:41 PM, Johnny Lu wrote: Hi. Is it a good idea to mimic NVE by a NVT simulation with a large temperature coupling time constant, to reduce the effect of the thermostat ? Not if your observable is the total energy. But for most interesting observables, this is more than fine. If I use V-rescale thermostat, what artifacts will the simulation get if I use a large coupling time (say, 500 ps) and single precision gromacs ? Probably nobody knows :-) Thermodynamic ensemble differences disappear as the system becomes large. But quantifying that from converged ensembles for a given observable is work. Mark Note also that, unlike averages, fluctuations are ensemble-dependent. Although v-rescaling (as most other thermostats) does indeed sample from the NVE ensemble in the mathematical limit of infinite coupling constant, this does not imply that, in practice, fluctuations converge to those in the NVE ensemble for large but finite coupling constants. As you can check in the v-rescaling paper, fluctuations were found to be very robust to changes of the coupling parameter (at least for the kinetic and potential energies). This is generally a good thing, but maybe not what you want to run a "fake" NVE simulation as you described. So, if you are interested in the fluctuations of some properties, you will have to check what is in practice their asymptotic behavior. Best, Antonio 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] Use NVT to mimic NVE
On Fri, Oct 10, 2014 at 7:41 PM, Johnny Lu wrote: > Hi. > > Is it a good idea to mimic NVE by a NVT simulation with a large temperature > coupling time constant, to reduce the effect of the thermostat ? > Not if your observable is the total energy. But for most interesting observables, this is more than fine. > If I use V-rescale thermostat, what artifacts will the simulation get if I > use a large coupling time (say, 500 ps) and single precision gromacs ? > Probably nobody knows :-) Thermodynamic ensemble differences disappear as the system becomes large. But quantifying that from converged ensembles for a given observable is work. Mark > 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] Use NVT to mimic NVE
seems to be a good idea, as the "canonical sampling through velocity rescaling" paper by G.Bussi said. arxiv.org/pdf/0803.4060 On Fri, Oct 10, 2014 at 1:41 PM, Johnny Lu wrote: > Hi. > > Is it a good idea to mimic NVE by a NVT simulation with a large > temperature coupling time constant, to reduce the effect of the thermostat ? > > If I use V-rescale thermostat, what artifacts will the simulation get if I > use a large coupling time (say, 500 ps) and single precision gromacs ? > > 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.
