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, [email protected] 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: [email protected] Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658
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