What do you mean by mutually inconsistent? From what I understand, they aren't.
Also, [bonds] type 6 won't work for what I want, since I don't want to keep the molecules at a fixed distance but to prevent them from coming closer, i.e. I want a potential that depends on the distance between the atoms. Testing the distance restraints can be quite exhaustive when you have about 160 restraints, and I am considering just the test case I'm trying, not the actual system which will have some more organic molecules, which will lead to a greater amount of combination of restraints... Thanks, João On Fri, Oct 9, 2009 at 12:51 AM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > João M. Damas wrote: > >> Gromacs users, >> >> I have a small test system of about 2500 atoms which consists on a few >> organic molecules in a box of water. I'm trying to use distance restraints >> to keep each molecule apart from each other and I've failed until now. >> >> I'll start by saying that the simulation runs smoothly without using >> distance restraints and that I've created a single molecule topology that >> describes all organic molecules, allowing the use of distance restraints. By >> applying just one distance restraint between two atoms of different >> molecules, the simulation still runs without problems. When I apply all the >> distance restraints I want, the system crashes in the first few steps with >> an XTC error, which is preceded by a few inconsistent shifts and some LINCS >> warnings. Varying the number of restraints that I use, makes the crash >> happen at later steps (500ish), meanwhile giving a lot of inconsistent >> shifts before crashing with a fatal error: Number of grid cells is zero. I >> know it seems I'm experimenting blindly, but varying the number of >> restraints was the first that occurred to me. >> I've searched the list for similar problems and tried a few more tests. >> I've turned off LINCS and reduced the time step and it didn't solve the >> problem, the box blew up after a few steps due to pressure problems. Since >> it could be a PBC problem, I tried to increase the size of the box, but it >> didn't solve the problem. Turning of PBC did solve the problem, but I really >> need PBC. I've also changed the low, up1 and up2 to values inferior to half >> the box size (I don't even care about the up1 and up2 values in this >> application, and I was setting them to 5.0 nm before), but it didn't solve >> the problem either. I'm a little on a dead end here and I was hoping anyone >> could give me some insight. >> >> By the way, I'm using GROMACS 4. >> > > The simplest explanation is that your sets of distance restraints are > mutually inconsistent. This destabilizes the system and eventually leads to > your symptoms. Consider using [bonds] type 6, per advice of manual section > 4.3.4. Either way, if you add these restraints one by one after testing that > the previous set seemed to work OK (didn't crash, trajectory looks right), > you may uncover your issue. > > Mark > _______________________________________________ > 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/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/mailing_lists/users.php > -- João M. Damas PhD Student Protein Modelling Group ITQB-UNL, Oeiras, Portugal Tel:+351-214469613
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