Sir, I have tried Berendsen barostat for Pcoupl. Still I get the same error.
Thank you, regards, Anu On Mon, Feb 25, 2013 at 6:58 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 2/25/13 12:16 AM, Anu Chandran wrote: > >> Dear users, >> I am trying to do a coarse grained simulation of an octamer of a 350 >> residue protein in water using gromacs-4.5.3 using martini force field. I >> got the following error when i started running NPT equilibration >> >> "Step 32, time 0.64 (ps) LINCS WARNING >> relative constraint deviation after LINCS: >> rms 16.561310, max 137.568573 (between atoms 626 and 627) >> bonds that rotated more than 30 degrees: >> atom 1 atom 2 angle previous, current, constraint length >> >> Step 32, time 0.64 (ps) LINCS WARNING >> relative constraint deviation after LINCS: >> rms 438.087891, max 3717.233887 (between atoms 580 and 581) >> bonds that rotated more than 30 degrees: >> atom 1 atom 2 angle previous, current, constraint length >> 626 627 121.9 0.2705 36.7207 0.2650 >> 621 622 90.0 0.2756 0.4600 0.2700 >> 624 626 91.5 0.3368 269.7515 0.3300 >> 621 623 90.0 0.2756 0.3172 0.2700 >> 620 624 90.4 0.3164 432.6003 0.3100 >> 622 623 90.0 0.2756 0.3991 0.2700 >> 618 620 85.5 0.3164 477.1006 0.3100 >> 626 627 121.9 0.2705 36.7206 0.2650 >> 615 618 88.6 0.3164 211.2461 0.3100 >> 607 610 141.3 0.3164 14.3253 0.3100 >> >> Step 32, time 0.64 (ps) LINCS WARNING >> relative constraint deviation after LINCS: >> rms 134.347206, max 2000.691284 (between atoms 4949 and 4946) >> bonds that rotated more than 30 degrees: >> atom 1 atom 2 angle previous, current, constraint length >> 610 612 149.2 0.3164 17.6610 0.3100 >> 612 614 89.7 0.3164 3.1394 0.3100 >> 614 615 150.9 0.3164 9.9306 0.3100 >> 615 618 88.6 0.3164 211.1131 0.3100 >> 618 620 85.5 0.3164 477.0737 0.3100 >> 620 624 90.4 0.3164 432.5994 0.3100 >> 4950 4949 75.8 0.3164 146.5132 0.3100 >> 624 626 91.5 0.3368 269.7514 0.3300 >> 4952 4950 118.9 0.3164 14.6303 0.3100 >> 468 469 90.0 0.2705 24.6834 0.2650 >> 4941 4939 90.0 0.3368 8.5601 0.3300 >> 585 586 61.3 0.2756 0.3361 0.2700 >> 4944 4941 82.5 0.3164 206.9830 0.3100 >> 586 587 90.1 0.2756 0.3137 0.2700 >> 4946 4944 90.0 0.3164 583.5660 0.3100 >> 606 607 90.0 0.3368 6.6314 0.3300 >> 4949 4946 90.0 0.3164 620.5243 0.3100 >> 580 581 91.9 0.4030 1003.9232 0.2700 >> 4954 4952 90.3 0.3164 1.6571 0.3100 >> 580 582 89.8 0.2756 960.9988 0.2700 >> 582 583 98.6 0.2756 592.0677 0.2700 >> 463 464 90.0 0.2654 7.6858 0.2600 >> 581 582 88.8 0.1280 193.0707 0.2700 >> 581 583 91.3 0.2254 514.1149 0.2700 >> Wrote pdb files with previous and current coordinates >> Wrote pdb files with previous and current coordinates >> Segmentation fault (core dumped)" >> >> >> Energy minimization and the NVT equilibration ran without any error or >> warning. The mdp file used is as shown below; >> >> title = Martini >> define = -DPOSRES >> integrator = md >> dt = 0.02 >> nsteps = 50000 >> nstcomm = 10 >> comm-grps = >> nstxout = 0 >> nstvout = 0 >> nstfout = 0 >> nstlog = 1000 >> nstenergy = 100 >> nstxtcout = 1000 >> xtc_precision = 100 >> xtc-grps = >> energygrps = Protein W >> nstlist = 10 >> ns_type = grid >> pbc = xyz >> rlist = 1.4 >> coulombtype = Shift >> rcoulomb_switch = 0.0 >> rcoulomb = 1.2 >> epsilon_r = 15 >> vdw_type = Shift >> rvdw_switch = 0.9 >> rvdw = 1.2 >> tcoupl = v-rescale >> tc-grps = System >> tau_t = 1.0 >> ref_t = 300 >> Pcoupl = parrinello-rahman >> Pcoupltype = isotropic >> tau_p = 5.0 >> compressibility = 3e-4 >> ref_p = 1.0 >> gen_vel = yes >> > > If you ran NVT previously, regenerating velocities defeats that purpose > and perturbs the system unnecessarily. Further, Parrinello-Rahman is not > very stable for initial equilibration; use Berendsen and then switch to P-R > for data collection. > > > gen_temp = 300 >> gen_seed = 473529 >> constraints = none >> constraint_algorithm = Lincs >> unconstrained_start = no >> lincs_order = 4 >> lincs_warnangle = 30 >> >> Also the water box after energy minimization showed some gaps towards the >> edge of the box when visualized using VMD. >> >> >> can anybody please help me on how to overcome this error? >> >> > In addition to the above, see the standard advice for unstable systems: > > http://www.gromacs.org/**Documentation/Terminology/**Blowing_Up<http://www.gromacs.org/Documentation/Terminology/Blowing_Up> > > -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<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<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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? 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