Hi Justin, Thanks for your response. After posting my query, I tried running the similar set with NPT run for 100 ps with sd integrator (with Pcoupl = berensen, tau_p = 0.5, compressibility = 4.5e-05, ref_p = 1.0) On giving berendsen instead of Parrinello-Rahman for pressure coupling, job finished successfully. Can you comment on this? As par the tutorial I am using simple vdW transformation only as mentioned below --------- couple-moltype = Methane ; name of moleculetype to decouple couple-lambda0 = vdw ; only van der Waals interactions couple-lambda1 = none ; turn off everything, in this case only vdW ---------
Thanks, Vivek On 09/02/2012, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > vivek sharma wrote: >> Hi There, >> I was trying to run a equilibrium run (npt) for system of "Methane in >> 1-octanol" (1 methane molecule with 200 1-octanol molecules with OPLS FF >> parameters). Following is the series of steps I followed: >> 1. Energy minimization with steep integrator for 5000 steps >> 2. Energy minimization with l-bfgs integrator for 5000 steps >> 3. NVT run for 100 ps with sd integrator >> 4. NPT run for 100 ps with sd integrator (with Pcoupl = >> Parrinello-Rahman, tau_p = 0.5, compressibility = 4.5e-05, ref_p = 1.0) >> >> During the NPT run I am ending up with following error (too many LINCS >> warning): >> --------------------------------------------- >> Step 25406, time 50.812 (ps) LINCS WARNING >> relative constraint deviation after LINCS: >> rms 11.778495, max 363.475445 (between atoms 2158 and 2157) >> bonds that rotated more than 30 degrees: >> atom 1 atom 2 angle previous, current, constraint length >> 2152 2150 90.0 0.1090 1.3690 0.1090 >> 2152 2151 90.0 0.1090 36.5266 0.1090 >> 2158 2156 90.0 0.1091 0.5637 0.1090 >> 2158 2157 90.0 0.2349 39.7278 0.1090 >> >> Back Off! I just backed up step25406b_n0.pdb to ./#step25406b_n0.pdb.1# >> >> Back Off! I just backed up step25406c_n0.pdb to ./#step25406c_n0.pdb.1# >> Wrote pdb files with previous and current coordinates >> Segmentation fault >> ------------------------------------------------------------ >> >> *.mdp files for above simulation are adapted from tutorial on free >> energy calculation by Justin. >> >> Please suggest me what could be wrong with above simulation. >> > > The answer for LINCS warnings is always the same - the system has become > unstable due to inappropriate geometry, bad .mdp settings, or a combination > of > both. To troubleshoot, start by turning off the free energy code to make > sure > your system is actually stable. If it's not, refer here: > > http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System > > If it is stable, turn back on whatever free energy settings you're using. I > assume, based on the tutorial, that this is a simple vdW transformation? > > -Justin > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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 > 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 > -- 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