Hi Justin, my mdp file for the md run looks like this: define = -DPOSRES integrator = md dt = 0.001 nsteps = 5000 nstxout = 100 nstvout = 0 nstfout = 0 nstlog = 1000 nstxtcout = 500 nstenergy = 5 energygrps = Protein Non-Protein nstcalcenergy = 5 nstlist = 10 ns-type = Grid pbc = xyz rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 0.9 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 gen_vel = yes gen_temp = 200.0 gen_seed = 9999 constraints = all-bonds tcoupl = V-rescale tc-grps = Protein System_&_!Protein tau_t = 0.1 0.1 ref_t = 298 298 pcoupl = no freezegrps = Protein_&_!TYP freezedim = Y Y Y
I added a phosphate (TYP) to my protein and now want to do first a minimization (which I already did), then a short md run (for the case that I am in a local minima) and after that again a minimization. Since I only want to minimize the energy of the phosphate I freezed the rest of the protein (Protein_&_!TYP). Since on my cluster I am not allowed to run long jobs I had to divide the minimization run in several runs. The output of the last run was: Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax < 10. Potential Energy = -7.7264606e+05 Maximum force = 1.6227990e+04 on atom 961 Norm of force = 1.2328220e+02 gcq#192: "It's So Fast It's Slow" (F. Black) Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax < 10. Potential Energy = -7.7264606e+05 Maximum force = 1.6227990e+04 on atom 961 Norm of force = 1.2328220e+02 After this minimization run I wanted to do the md run. My protein is a membrane protein with its surrounding membrane. I already did a minimization and md run with this protein but without the phosphate. The only difference to the time when everything worked fine is the phosphate. Does this help you somehow to see the failure? Thank you!! > > > On 9/12/12 6:57 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: >> Hi everybody, >> during the mdrun_mpi I get many LINCS warnings like for example: >> >> Step 1143, time 1.143 (ps) LINCS WARNING >> relative constraint deviation after LINCS: >> rms 0.265373, max 1.416702 (between atoms 976 and 979) >> bonds that rotated more than 30 degrees: >> atom 1 atom 2 angle previous, current, constraint length >> 976 979 90.0 0.1072 0.2320 0.0960 >> >> >> But I don't know why. I already minimized my protein. And also in the >> grompp run there were no error messages. This was the end of my grompp >> output: >> >> >> processing index file... >> Making dummy/rest group for Acceleration containing 80212 elements >> Making dummy/rest group for Freeze containing 51274 elements >> Making dummy/rest group for VCM containing 80212 elements >> Number of degrees of freedom in T-Coupling group System is 102623.00 >> Making dummy/rest group for User1 containing 80212 elements >> Making dummy/rest group for User2 containing 80212 elements >> Making dummy/rest group for XTC containing 80212 elements >> Making dummy/rest group for Or. Res. Fit containing 80212 elements >> Making dummy/rest group for QMMM containing 80212 elements >> T-Coupling has 1 element(s): System >> Energy Mon. has 2 element(s): Protein non-Protein >> Acceleration has 1 element(s): rest >> Freeze has 2 element(s): Protein_&_!TYP rest >> User1 has 1 element(s): rest >> User2 has 1 element(s): rest >> VCM has 1 element(s): rest >> XTC has 1 element(s): rest >> Or. Res. Fit has 1 element(s): rest >> QMMM has 1 element(s): rest >> Checking consistency between energy and charge groups... >> Estimate for the relative computational load of the PME mesh part: 0.32 >> writing run input file... >> >> >> Can you please help me? > > http://www.gromacs.org/Documentation/Terminology/Blowing_Up > > Without a complete description of your system (its contents, previous > minimization and equilibration and their success/failure) and any relevant > .mdp > file(s), there's little else that anyone can say. > > -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 > * 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