I thought that the problem is with atom 18. Allright, I'll go through the protocol again .
Thanks Justin. Sincerely, Shima ----- Original Message ----- From: Justin Lemkul <jalem...@vt.edu> To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Saturday, July 28, 2012 5:25 PM Subject: Re: [gmx-users] Diagnoding + system blowing up On 7/28/12 7:34 AM, Shima Arasteh wrote: > > > Hi all, > > My system has got BLOWING UP . I followed the protocol in > http://www.gromacs.org/Documentation/Terminology/Blowing_Up and got as below: > > Step 1: If the crash is happening relatively early (within a few steps), set > nstxout (or nstxtcout) to 1, capturing all possible frames. Watch the > resulting trajectory to see which atoms/residues/molecules become unstable > first. > I got this warning: > Warning: 1-4 interaction between 5 and 18 at distance 2.003 which is larger > than the 1-4 table size 2.000 nm > The output shown has nothing to do with the suggested diagnostic step. At what time step does this occur? Have you done what "Step 1" suggests, and if so, have you watched the resulting trajectory to see what happens? > Step 2: Simplify the problem: > If you have a new box of solvent, try minimizing and simulating a single > molecule to see if the instability is due to some inherent problem with the > molecule's topology or if instead there are clashes in your starting > configuration. > > I got this: > Now there are 24 residues with 360 atoms > Making bonds... > Warning: Long Bond (1-18 = 0.357049 nm) > Again this output is not really relevant to the suggested "Step 2" - this is from pdb2gmx. What are atoms 1 and 18? It seems that the starting geometry is very poor. Long bonds indicate missing residues or atoms or just a bad configuration. > Step 3: Monitor various components of the system's energy using g_energy. If > an intramolecular term is spiking, that may indicate improper bonded > parameters, for example. > > The improper-dihedral plot is strange. It "goes up in first picoseconds" and > then goes down slightly. > > I think there is something wrong in dihedrals which I defined in .rtp file in > the new residue. atom 18 is the H atom of formyl ( Formyl is as the > N-terminus and is connected to a Valine residue) > Now , what do I need to do? Going to the next step of diagnosing? or no? How > can I fix the problem? > I think you need to back up and do some relevant investigating in steps 1 and 2 first. You haven't really followed any of the advice given thus far so you're sort of shooting in the dark. Something is clearly wrong either in the topology or the starting configuration, but it is not apparent at this point which it is. -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * 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
