renying wrote: > Hello, everyone. > I have loaded a pdb file of protein complex from Protein Data Bank and put it > into water soltion with pdb2gmx, editconf and genbox. > After 400 steps of energy minimization when the potential energy seems to be > more or less stable, I want to do position restraints. However, it always > failed. > > The error info is as follows: > Step 1, time 0.002 (ps) LINCS WARNING > relative constraint deviation after LINCS: > max 0.000645 (between atoms 13241 and 13242) rms 0.000043 > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 13241 13242 31.2 0.1000 0.0999 0.1000 > > t = 0.002 ps: Water molecule starting at atom 73326 can not be settled. > Check for bad contacts and/or reduce the timestep.Wrote pdb files with > previous and current coordinates > Large VCM(group System): 0.03330, -0.01095, -0.00024, ekin-cm: > 2.20013e+03
Check out http://wiki.gromacs.org/index.php/Errors#LINCS_warnings for some ideas. Looking at this water molecule's environment can help. > The system seems to be exploding. I have tried the follwing parameters and > sadly, none of them works. > nsteps = 200/400/800/1000 steps in em.mdp > dt = 0.002/0.001/0.0002 ps in pr.mdp > tc-grps = Protein SOL or > tc-grps = system in pr.mdp > tau_t = 0.002 0.002 or longer time in pr.mdp If you're sure the problem isn't a water trapped inside a protein or suchlike, one thing you can try is a slow heating. You'll need to do a series of .mdp files with an initial gen_vel to (e.g.) 50K, and then use ref_t to increase that in similar increments. > The total charge of the system is -273.000 e and I didn't neutralize it for > some reasons. Does this matter much? It probably isn't breaking the numerical simulation, but it could well mean you're not modelling reality. Nature abhors a vacuum, and an isolated charge :-) Mark _______________________________________________ gmx-users mailing list [email protected] http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
