Dear Justin, thank you for your precious help. Yes, the problem is what you say and what I was suspecting too (but I was not sure, that's why I was searching for a confirmation of my suspects from more expert people). The problem however is present in the NVT->NPT junction. My .mdp settings were NVT: tinit = 0 init_step = 0 nsteps = 10000 dt = 0.002
NPT tinit = 0 init_step = 20000 (instead of 10000) nsteps = 50000 dt = 0.002 That's why I had a last NPT step of 70000 instead of 60000, and that's why I set init_step = 70000 in the production MD. What you are saying also explains the anomalous behaviour of the xvg file created from the .edr file, in which only few points were saved, therefore the graphs created with xmgrace contain only 7 values (at 140, 200, 300 400, 5140, 10140, 15140 ps). I always set nstep identical to the last step of the previous equilibration MD because I understood that it was necessary to do it to obtain an exact continuation, there is no other special reason. Since you are saying that this is no (longer?) necessary (I'm currently using Gromacs 4.0.7 on this machine), I'm very happy to set always nsteps = 0, to avoid future mistakes. In the meantime, what I have to do? I had a look at the .xtc files with gmxcheck and apparently all is fine, with no error messages, also the trajectory seems to be coherent with my expectations. I run g_rms and g_gyrate and the behaviour of the systems appears "normal" (apart from the fact that the system is not stabilized yet, so I have to continue the trajectory). I can provide you (offlist) the .xvg graphs, if you want. Based on these data, what do you suggest to do? Do you think that the simulation could be considered formally correct (i.e. this is only a problem of erroneous writing of .edr file) or do I have to repeat (AAAAAARRRRRRGGGGHHHHH) the whole simulation? I saw in the manual that the option -rerun of mdrun command allows to recalculate forces and energies from a trajectory file, do you think that I can use it to obtain a new .edr file? Thank you as usual for your invaluable help Anna PS: i'm asking just another suggestion, to the gmx-users administrators. I receive the mails from gmx-users list in form of digest. How can I do to reply to messages extracted from the digest in order to create a continuous thread in the archive? At present, I'm making a reply to the digest message in order to keep the gmx-users list updated, but it seems to me that the messages are stored as separated. ---------------------------------------------------------------------- Message: 1 Date: Wed, 27 Apr 2011 11:18:51 -0400 From: "Justin A. Lemkul" <jalem...@vt.edu> Subject: Re: [gmx-users] Md continuation with cpt To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <4db833db.4050...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Anna Marabotti wrote: > Dear gmx-users, > since I'm sending my simulations to a system with a queue with a > wallclock time of 24 h, I necessarily have to simulate small parts of my > simulation, that I "stick" together at the end with trjconv. To continue > my simulations, I'm using the .cpt file. Here my settings concerning the > number of steps, dt etc. Since I started the full MD after 20 ps NVT and > 100 ps NPT I set the mdp file as: > > integrator = md > dt = 0.002 > nsteps = 2500000 (total 5 ns - the max time compatible with the > wallclock time) > init_step = 70000 (the last step after NVT+NPT) Is it? 120 ps/0.002 ps = 60000 steps. <snip> > Opened 1R3Afull20ns.edr as double precision energy file > frame: 0 (index 0), t: 140.000 Based on this output, frame 0 corresponds to a time of 140 ps, as set by your init_step * dt. > Reading energy frame 2 time 300.000 > Timesteps at t=200 don't match (60, 100) It looks like the setting for nstenergy is causing frames to be written at integral multiples of 100 ps, rather than init_step + nstenergy. So you have frame 0 at 140 ps, frame 1 at 200 ps, then 100-ps intervals until... > Reading energy frame 50 time 5100.000 > Timesteps at t=5100 don't match (100, 40) > etc. > Timesteps at t=5140 don't match (40, 60) > > Timesteps at t=5200 don't match (60, 100) > Reading energy frame 100 time 10000.000 > Timesteps at t=10100 don't match (100, 40) > > Timesteps at t=10140 don't match (40, 60) > > Timesteps at t=10200 don't match (60, 100) > Reading energy frame 150 time 14900.000 > Timesteps at t=15100 don't match (100, 40) > > Timesteps at t=15140 don't match (40, 60) > > Timesteps at t=15200 don't match (60, 100) > Last energy frame read 198 time 19600.000 > All of these mismatches seem to agree with the above theory. The difference is always 40 or 60, the remainder of some break between your value determined by init_step and initial time of 140 ps. > Found 199 frames. > > gcq#131: "Royale With Cheese" (Pulp Fiction) > I don't understand why there are so many mismatches in my file. Moreover > all but one are in the correspondence of the "junctions" I made between > two consecutive 5 ns runs. Does it depend on some settings regarding > init_step or dt or tinit in the .mdp file? Did I make correctly the > continuation? Could somebody help me to find the error? Is there some reason you needed the trajectory to start at 140 (120?) ps? Usually a new trajectory is intitiated with init_step = 0. Continuing a run using while still maintaining the previous ensemble does not necessarily need init_step > 0. It is possible this is a bug related to nst*out/energy/log being writing every 50000 steps and assuming init_step = 0 (i.e. writing at 100 ps rather than 240 ps, based on your initial settings). What version of Gromacs is this? -Justin > Many thanks in advance and best regards > Anna > > __________________________________________________________________ > Anna Marabotti, Ph.D. > Laboratory of Bioinformatics and Computational Biology > Institute of Food Science - CNR > Via Roma, 64 > 83100 Avellino > Phone: +39 0825 299651 > Fax: +39 0825 781585 > E-mail: amarabo...@isa.cnr.it <mailto:amarabo...@isa.cnr.it> > Skype account: annam1972 > Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm > > "When a man with a gun meets a man with a pen, the man with the gun is a > dead man" > (Roberto Benigni, about Roberto Saviano) > > -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== ------------------------------ Message: 2 Date: Wed, 27 Apr 2011 11:21:19 -0400 From: "Justin A. Lemkul" <jalem...@vt.edu> Subject: Re: [gmx-users] Md continuation with cpt To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <4db8346f.8030...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Justin A. Lemkul wrote: > It is possible this is a bug related to nst*out/energy/log being writing > every 50000 steps and assuming init_step = 0 (i.e. writing at 100 ps > rather than 240 ps, based on your initial settings). What version of > Gromacs is this? Actually, this wouldn't be considered a bug. If you're telling grompp that you've done 70000 steps previously, the input will then expect that these frames exist, and the output is always written every nst*out/energy/log steps. Thus, all intervals of the concatenated trajectory or energy files should have consistently spaced frames. In your case, this is not true. -Justin -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- 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
