Hi, In the past few weeks, I have run some simulations of 254 water molecules. Although I got some results, I did not do things in the best way. For example, I threw away my equilibrated ensemble before doing my production run, as was kindly pointed out to me on this mailing list last week. In trying to think more carefully about the input parameters and the commands I use, I have done some more reading, particularly in the very helpful lysozyme tutorial (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lyso zyme/index.html) by Justin Lemkul.
In planning another simulation, I would like to understand better reasonable parameters to use and the correct commands to use. If you have time, can you please look at the pdf file at http://www.andrew.cmu.edu/user/adeyoung/may28.pdf that I have created? If you have time, I have some questions about it. On page 1, I have typed some possible parameter files (adapted from Justin Lemkul's lysozyme tutorial); on page 2, I have typed a list of commands (also adapted from the lysozyme tutorial) I may use in my run. I plan to do energy minimization, NPT equilibration, and NPT MD (for NPT, I plan to use Berendsen pressure coupling and Nose-Hoover temperature coupling) using Gromacs 4.5.4. If you have time, here are my questions about the pdf file: --- (i) In equilibration, what is a reasonable value of nstlist to use? The Gromacs manual on page 18 says that "nstlist is typically 10," but is it true that, in principle, the smaller that nstlist is (that is, the more often the pairlist is updated), the more accurate the simulation is, at greater computational cost? As a rule of thumb, should I use nstlist = 10 or something smaller? I have access to a cluster, so I don't have too many worries about computational cost, to a reasonable extent. (ii) In equilibration, what is a reasonable value of the time constant tau_p to use for Berendsen pressure coupling? The default is 1 ps, although I have seen tutorials where people use tau_p as high as 2 ps or as low as 0.1 ps. The Gromacs manual on page 32 gives a relationship for the change in pressure with respect to time for Berendsen pressure coupling: dP/dt = (P_0 - P)/tau_p where P_0 is the reference pressure (ref_p in Gromacs). So it seems that the smaller the tau_p, the faster the pressure relaxes toward the reference pressure. So, naively, it would be best to use a small tau_p. However, am I correct in thinking that, on the other hand, if I make tau_p too small for a fixed step size dt, significant inaccuracies may result? (iii) In equilibration, is it reasonable to set DispCorr = no? I won't be using my equilibration results for any detailed analysis; I only wish to generate a (hopefully) reasonable ensemble and relax the pressure to the reference pressure. (iv) Similarly, in production, is it reasonable to set DispCorr = no? I suppose that it depends on what one ultimately wants to calculate using the final MD production results. Since I am still at the stage of getting familiar with Gromacs, I will be doing only simple analyses (RDF, MSD, velocity autocorrelation function, and extracting plots of pressure and density versus time from the final edr file); I will not be doing complicated free energy calculations, for example. (v) What does the continuation parameter do? Looking under section 7.3.18 (the section called "Bonds") on page 181 of the Gromacs manual, it seems that this is mainly if I choose to constrain particular atoms or bonds. Here, since my system consists only of water, I will not use any constraints, I think. However, I am getting myself confused, I think. I do, in fact, want my (NPT) MD production run to be a "continuation" of my (NPT) equilibration; does this mean that the continuation parameter should be set to "yes"? I am not sure, because I am not sure if the continuation parameter is exactly relevant to whether my production run is a "continuation" of my equilibration (that is, I want my production run to use the ensemble that was created during equilibration). (vi) On page 2 of my pdf file, I have highlighted parts of steps (6) and (7) in magenta. Could you please look at these parts and help me see whether or not I am using the correct commands to, firstly, create a checkpoint file at the end of equilibration and to, secondly, use that checkpoint file as input into the grompp step of my MD production run? About a week ago, Justin pointed out that I should use the -t option in the grompp program to do this. But, I want to make sure that I understand correctly... ...In the entry for grompp in the Gromacs manual (for example, see http://manual.gromacs.org/current/online/grompp.html or page 300 in the manual), the listing for -t says "Full precision trajectory: trr trj cpt" in the description column. Does this mean that I can give grompp EITHER the previous trr trajectory file OR the cpt checkpoint file that I created using -cpo in equilibration? Or must I definitely pass the cpt file to grompp in order to continue using in production the ensemble that was created during equilibration? --- Thank you very much for your time! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing list gmx-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
