Dear All, Thanks a lot to Mark,Tsjerk and Erik your promt reply. It is a globular protein containing approximately 70 residues having crysal structure, without any ligand,the simulation continued for 1.5 ns, & then gave the segmentation fault, My .mdp file is given below, I used SPC216 water and steepest descent for minimisation, the emtol was 1000,it converged to that within 800 steps.I used position restrained dynamics for 50ps.The protein had -ve charge, so I added NA+ as counter ion.I used the same parameter for carrying out the simualtion of the same protein at 3/4 other tempeartures,the runs were completed without giving any error.Waiting for your promt help.
title = Yo cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 5000000 ; total 10 ns nstcomm = 1 nstxout = 250 nstvout = 1000 nstfout = 0 nstlog = 100 nstenergy = 100 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb = 1.0 rvdw = 1.0 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = Protein SOL NA+ tau_t = 0.1 0.1 0.1 ref_t = 523 523 523 ; Energy monitoring energygrps = Protein SOL ; Isotropic pressure coupling is now on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is off at 300 K. gen_vel = no gen_temp = 523.0 gen_seed = 173529 regards Sangeeta --- Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote: > Hi Sangeeta, > > It would be helpful to us if you gave more > information than "I tried > to run a simulation and it crashed". What kind of > protein, any > ligands/non-standard groups. Did you perform energy > minimization, etc, > etc, etc... What's in the .mdp file? > > Tsjerk > > On 3/15/07, Erik Marklund <[EMAIL PROTECTED]> > wrote: > > > > > > 15 mar 2007 kl. 08.29 skrev sangeeta kundu: > > > > Dear all, > > I gave a simulation run of a protein using > G43a1force field at 523K > > using Berendson's Temperature coupling for 10 > ns, But three times it > > failed with the messege "segmentation fault" , > without giving any other > > error messege. Previously I ran the simualtion of > the same protein at lower > > temperature, (upto 473K) , and in all cases it ran > successfully, but when I > > used the temperature of 523 K it failed, I can not > debug, please help. > > > > > > I'm no expert, but I think a shorter timestep > could be required for the > > integrator to be stable when using such high > temperatures, since the atoms > > will move around quite fast. > > > > > > > > I have another question, Is there any way of > analysing hydrogen bonds > > on a residue basis? I mean to say how can I get > the distribution of HBond > > over residue number, I looked at g_hbond , but I > could not get it. > > > > > > It requires some postprocessing of the data, but > the hbn- and hbm-output of > > g_hbond together contains what you need to know > about the hydrogen bonds on > > an atom index basis. Now, you can easily go from > the level of atoms to the > > level of residues. > > > > > > > > regards > > Sangeeta > > > > ________________________________ > > Here's a new way to find what you're looking for > - Yahoo! Answers > > _______________________________________________ > > gmx-users mailing list [email protected] > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don't post (un)subscribe requests to the > list. Use the > > www interface or send it to > [EMAIL PROTECTED] > > Can't post? Read > > http://www.gromacs.org/mailing_lists/users.php > > > > _______________________________________________ > > Erik Marklund, PhD student > > Laboratory of Molecular Biophysics, > > Dept. of Cell and Molecular Biology, Uppsala > University. > > Husargatan 3, Box 596, 75124 Uppsala, Sweden > > phone: +46 18 471 4537 fax: +46 18 511 755 > > [EMAIL PROTECTED] > http://xray.bmc.uu.se/molbiophys > > > > > > _______________________________________________ > > gmx-users mailing list [email protected] > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don't post (un)subscribe requests to the > list. Use the > > www interface or send it to > [EMAIL PROTECTED] > > Can't post? Read > > http://www.gromacs.org/mailing_lists/users.php > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > Junior UD (post-doc) > Biomolecular NMR, Bijvoet Center > Utrecht University > Padualaan 8 > 3584 CH Utrecht > The Netherlands > P: +31-30-2539931 > F: +31-30-2537623 > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the > list. Use the > www interface or send it to > [EMAIL PROTECTED] > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > __________________________________________________________ Yahoo! India Answers: Share what you know. Learn something new http://in.answers.yahoo.com/ _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
