Sorry, I forgot to change the subject of my previous mail. Anna -----Messaggio originale----- Da: Anna Marabotti [mailto:anna.marabo...@isa.cnr.it] Inviato: martedì 28 giugno 2011 12.09 A: 'gmx-users@gromacs.org' Oggetto: R: gmx-users Digest, Vol 86, Issue 183
Dear Tsjerk, dear all, thank you very much for suggestion. One of the main reasons why I never used the rhombic dodecahedron box for my simulations is the fact that it is really hard to visualize the results with programs such as VMD or Pymol, and therefore I cannot check easily during the setting of my system if the work proceeds properly. Since I would like to redo my simulations following your suggestion, could you please give me some hints on how to proceed in order to visualize easily the system? For example, now I created a dodecahedric box filled with water and ions. I tried to visualize it with VMD and I saw it as a rectangular box with the protein at one edge. I tried to use the command trjconv: trjconv -f prot_dod_box_neu.gro -s prot_dod_box_neu.tpr -o prot_dod_box_neu2.gro -pbc mol -ur compact and I obtained an error message stating: Fatal error: Index[84328] 84329 is larger than the number of atoms in the trajectory file (84328) I don't find this error neither in the gmx-users list archive (indeed it's becoming harder and harder to search into this archive, given that each message is visualized 10 times, as I already noticed sometimes ago), nor in the Error section. The first .gro file is the one coming from genion, and the .tpr file is the one I used to neutralize the system, which is the .tpr file I should give to trjconv? You see, if every time I try to use a box different from the standard cubic one I has to deal with such maybe trivial (for you) problems, but difficult and long to solve, I'm quite discouraged to use it! This is also a kind request for Gromacs Web site managers: could you please add a section for this (recurrent, I suspect) problem of box visualization in the "How-to" section? it would be very useful for users, I think, and probably also for you (less trivial questions posted to the gmx-users list...) Many thanks in advance for the help you could provide me. Anna Message: 6 Date: Mon, 27 Jun 2011 17:05:17 +0200 From: Tsjerk Wassenaar <tsje...@gmail.com> Subject: Re: [gmx-users] about periodic images violation To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <banlktim3r1339yb6eckedf9etyrg+q+...@mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Hi Anna, The spikes you see occur because the protein is broken over the periodic boundaries. Not hard to see that a broken molecule will have a minimal minimal distance. The other problem may well occur due to rotation of your molecule. Since you set -bt tric, you just get a rectangular unit cell, which has the drawback that the shortest distance may not be long enough to keep the protein from self-interactions in certain orientations. I know it's considered a pretty standard setup, which is why I mentioned it before. You should use a rhombic dodecahedron. With a rectangular cell, you could even have self-interaction in a nastier way: the ends of the protein can try to avoid each other, rather than align with each other. That would result in an altered ensemble, yet one in which you wouldn't see violations of the minimal distance. In a rhombic dodecahedron the spatial distribution is much more uniform... Cheers, Tsjerk On Mon, Jun 27, 2011 at 12:48 PM, Anna Marabotti <anna.marabo...@isa.cnr.it> wrote: > Dear gmx-users, > I'm inserting into the discussion about periodic images since I'm > experimenting a problem of minimum distance violation too. I'm doing > simulations on a dimeric protein (with no covalent bonds between the two > subunits) which derives not from a crystallographic structure but from a > model. I made several simulations changing the gen_seed in order to explore > deeply the conformational space of the protein. I used a triclinic box > (option editconf -bt triclinic -d 1 -c) filled with spc water and > neutralized with ions; in my opinion, it's quite a standard system. I > equilibrated the system with a minimization (emtol = 500 reached) and with > NVT+NPT in position-restrained mode (20+100 ps) at 310 K, then launched the > full MD for 30 ns, always at 310 K. I repeated this procedure > (NVT+NPT+FullMD) for each of the gen_seed assigned (random numbers), > starting from the same minimized structure. Obviously, in PR-NPT and full Md > simulations, I did not recalculated the initial velocity (it's a > continuation). Before starting with full MD I checked for energetic > parameters in .edr file (Pot, Kin, Tot, T, P) and all seem stable with no > apparent problems. I run the 30 ns simulations and now I'm checking for the > results. > Looking at the trajectories I see that in some (but not all) cases, the > protein moves from the center of the box to one of the edges, starting from > a time that is different in each simulation, when it happens. I run > g_mindist, and in some cases (generally when the protein doesn't move so > much) I see some "spikes" in the plot (that disappear if I apply trjconv > -pbc nojump to the trajectory), but apart from these "spikes" the minimum > periodic distance in the trajectory is at least 1.5 nm (I set van der Waals > cut-off at 1.4 nm). In other cases, however (essentially when the protein > starts moving towards the edges of the box), the minimum periodic distance > starts decreasing (in some simulations after 10 ns, in some simulations > after 20: there is not a common point after which you can see a sudden > decrease of minimum periodic distance of the system) and reaches a value > below 1.4 nm or even below 1 nm. Considering that the starting system is > more or less the same in all cases, I don't identify the reason why the > system "behaves" like this, and moreover what can I do to avoid this. My > questions are: > - do I have to enlarge the box? but I don't think that this would solve the > "motion" of the protein towards one edge of the box > - do I have to change the box? In his last message Tsjerk suggests to use a > rhombic dodecahedron box, could it be useful in my case? > - do you think it's a problem of stabilization of the system? Should I run a > deeper minimization, or a longer NVT+NPT in my system? > I'm quite puzzled especially because the system is the same in all cases, > the only thing I changed in my simulations is the gen_seed. > Could anybody give me some suggestions about it? > Thank you very much > Anna > > > > > -- > 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 > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands ------------------------------ -- 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! End of gmx-users Digest, Vol 86, Issue 183 ****************************************** -- 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
