Re: [gmx-users] Unexpected results arising from T- and P-coupling methods
Hello, I have also realized similar behaviour: NpT simulations performed with a Berendsen barostat give lower densities than simulations coupled with P-R. However I think this is due to the fact that I never achieve a pressure of 1bar (it is always around 1.2bar) with P-R even after a previous equilibration of 40ns. I am aware that pressure is a strongly fluctuating quantity and this topic has been discussed for several times on the list, but the equations of motion for the box size given by the Lagrangian for P-R should finally give an average pressure of 1bar even if the fluctuations are large. So what I assume is, that the Leap-Frog integrator is not suitable for this coupling scheme, BUT THIS IS JUST AN ASSUMPTION I DO NOT KNOW, and unfortunately I had no time to try and validate this, yet. /Flo On Tue, 2011-04-12 at 09:13 -0400, chris.ne...@utoronto.ca wrote: > I can't tell you if there is a problem or not. > > The only intended difference that I can see is that for 4.5.X: > > # grompp by default sets the new nsttcouple parameter equal to > nstlist, this means T-coupling is done less frequently; grompp checks > if tau_t is large enough > # grompp by default sets the new nstpcouple parameter equal to > nstlist, this means P-coupling is done less frequently; grompp checks > if tau_p is large enough > > (see http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.5.x ) > > Note that there were some fixes to P-R scaling in the 4.0.X series -- > se http://www.gromacs.org/About_Gromacs/Release_Notes/Revisions_in_4.0 > > To test this further, I suggest that you need to define a good > procedure to ensure that what you are seeing is (b) from a well > equilibrated system and is also (b) statistically significant. > > I suggest that one way to do this is to cycle through your T- and P- > coupling options at a given temperature. For example, at T=500 K, run > X ns of Berendsen, then X ns of Parrinello-Rahman, then back to > Berendsen, and so on for a few cycles. Each time you switch coupling > method, be sure to use the structure output from the previous run. > Also be sure that X ns is as long as you can afford. This way, you > will be able to pick out systematic changes as temperature/density > oscillations with periods that are related to your changes of > algorithm. This also ensures that what you are seeing is not simply an > artifact of having a poorly equilibrated density in your initial > structure. > > You could also run the same cycle with Berendsen and V-rescale. > > Chris. > > -- original message -- > > Dear gmxers, > According to my recent practice, we find that the Berensen methods > for T- and P- coupling can yield reasonable averaged density as a > function of temperature, but when the v-rescale method and the > Parrinello-Rahman method are employed for T- and P- coupling, somewhat > unexpected results (i.e. density at higher temperature is bigger than > that at lower tempearature) are obtained. Generally, the latter setup > is considered to be prefered to the former one in simulating realistic > ensemble. I am using gmx-4.5.3, and previously I have also performed > one similar work using 4.0 which can generate expected results using > the latter setup. I wonder if this version 4.5.3 has some bugs in > calculating T and P, and are they dealt with in 4.5.4? Please give me > some hints. > > Yours sincerely, > Chaofu Wu, Dr. >-- >Department of Chemistry and Materials Science, Hunan University of > Humanities, Science and Technology, Loudi 417000, the People?s > Republic of China (P.R. China) > -- next part -- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110412/ceadf085/attachment.html > > -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Unexpected results arising from T- and P-coupling methods
I can't tell you if there is a problem or not. The only intended difference that I can see is that for 4.5.X: # grompp by default sets the new nsttcouple parameter equal to nstlist, this means T-coupling is done less frequently; grompp checks if tau_t is large enough # grompp by default sets the new nstpcouple parameter equal to nstlist, this means P-coupling is done less frequently; grompp checks if tau_p is large enough (see http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.5.x ) Note that there were some fixes to P-R scaling in the 4.0.X series -- se http://www.gromacs.org/About_Gromacs/Release_Notes/Revisions_in_4.0 To test this further, I suggest that you need to define a good procedure to ensure that what you are seeing is (b) from a well equilibrated system and is also (b) statistically significant. I suggest that one way to do this is to cycle through your T- and P- coupling options at a given temperature. For example, at T=500 K, run X ns of Berendsen, then X ns of Parrinello-Rahman, then back to Berendsen, and so on for a few cycles. Each time you switch coupling method, be sure to use the structure output from the previous run. Also be sure that X ns is as long as you can afford. This way, you will be able to pick out systematic changes as temperature/density oscillations with periods that are related to your changes of algorithm. This also ensures that what you are seeing is not simply an artifact of having a poorly equilibrated density in your initial structure. You could also run the same cycle with Berendsen and V-rescale. Chris. -- original message -- Dear gmxers, According to my recent practice, we find that the Berensen methods for T- and P- coupling can yield reasonable averaged density as a function of temperature, but when the v-rescale method and the Parrinello-Rahman method are employed for T- and P- coupling, somewhat unexpected results (i.e. density at higher temperature is bigger than that at lower tempearature) are obtained. Generally, the latter setup is considered to be prefered to the former one in simulating realistic ensemble. I am using gmx-4.5.3, and previously I have also performed one similar work using 4.0 which can generate expected results using the latter setup. I wonder if this version 4.5.3 has some bugs in calculating T and P, and are they dealt with in 4.5.4? Please give me some hints. Yours sincerely, Chaofu Wu, Dr. -- Department of Chemistry and Materials Science, Hunan University of Humanities, Science and Technology, Loudi 417000, the People?s Republic of China (P.R. China) -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110412/ceadf085/attachment.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Unexpected results arising from T- and P-coupling methods
Dear gmxers, According to my recent practice, we find that the Berensen methods for T- and P- coupling can yield reasonable averaged density as a function of temperature, but when the v-rescale method and the Parrinello-Rahman method are employed for T- and P- coupling, somewhat unexpected results (i.e. density at higher temperature is bigger than that at lower tempearature) are obtained. Generally, the latter setup is considered to be prefered to the former one in simulating realistic ensemble. I am using gmx-4.5.3, and previously I have also performed one similar work using 4.0 which can generate expected results using the latter setup. I wonder if this version 4.5.3 has some bugs in calculating T and P, and are they dealt with in 4.5.4? Please give me some hints. Yours sincerely, Chaofu Wu, Dr. -- Department of Chemistry and Materials Science, Hunan University of Humanities, Science and Technology, Loudi 417000, the People’s Republic of China (P.R. China)-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
