Thanks a lot of suggestions. Now my simulation is running without any errors. I have decreased the box dimension (by using -d 1.2 in editconf) and also by using cutoff with rlist=rvdw=rcoulomb=1.0. Now there is no warning or errors in nvt and npt equilibration.
Thank you, with regards, Anu On Thu, Feb 21, 2013 at 10:32 AM, Emanuel Birru <emanuel.bi...@monash.edu>wrote: > > Correction on #6 > 6. if that doesn't help decrease your time step. > Sorry for the confusion :) > > Cheers, > EB > -----Original Message----- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] > On Behalf Of Anu Chandran > Sent: Thursday, 21 February 2013 3:34 PM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] Re: A note while running grompp for nvt > equilibration > > Sir, > I tried using cutoff for van der Waals interactions. I got the following > error during the nvt equilibration: > > > "step 0, time 0 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 0.040332, max 2.236585 (between atoms 24073 and 24072) bonds that > rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length Wrote pdb > files with previous and current coordinates > > Step 0, time 0 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 0.005594, max 0.252567 (between atoms 24347 and 24344) bonds that > rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 24349 24347 34.7 0.1517 0.1322 0.1250 > 24383 24381 39.0 0.2108 0.1438 0.1340 > 24382 24381 31.8 0.1027 0.1089 0.1010 > 24387 24383 32.0 0.2041 0.1399 0.1340 > 24388 24387 30.3 0.2493 0.1070 0.1010 > 24344 24342 54.8 0.2383 0.1843 0.1529 > 24347 24344 49.3 0.2560 0.1906 0.1522 > 24346 24344 50.0 0.2082 0.1295 0.1090 > 24345 24344 56.2 0.1728 0.1357 0.1090 > 24063 24061 34.7 0.2181 0.1461 0.1335 > 24072 24063 39.2 0.1828 0.1480 0.1449 > starting mdrun 'Protein in water' > 50000 steps, 100.0 ps. > > Step 0, time 0 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 9.003327, max 419.005005 (between atoms 24380 and 24378) bonds that > rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 24381 24378 97.3 0.1825 59.6595 0.1463 > 24380 24378 122.0 0.1260 45.7805 0.1090 > 24379 24378 111.1 0.1319 28.6967 0.1090 > 24073 24072 90.2 0.3528 0.8138 0.1090 > 24349 24347 89.7 0.1517 46.2536 0.1250 > 24348 24347 95.7 0.1756 13.5872 0.1250 > 24383 24381 86.4 0.2108 5.1830 0.1340 > 24382 24381 105.2 0.1027 2.7271 0.1010 > 24387 24383 85.2 0.2041 2.1027 0.1340 > 24384 24383 88.3 0.0874 2.5321 0.1340 > 24386 24384 92.8 0.1068 3.6505 0.1010 > 24385 24384 88.0 0.0997 3.7036 0.1010 > 24389 24387 88.7 0.2448 1.5454 0.1010 > 24388 24387 88.4 0.2493 1.5186 0.1010 > 24368 24366 74.3 0.1338 0.2409 0.1335 > 24367 24366 104.8 0.1231 0.0883 0.1229 > 24370 24368 103.0 0.1458 5.0355 0.1449 > 24369 24368 96.3 0.1012 0.2541 0.1010 > 24390 24370 121.9 0.1532 4.8700 0.1522 > 24371 24370 97.9 0.1097 5.0227 0.1090 > 24375 24372 80.9 0.1936 9.2201 0.1529 > 24374 24372 92.0 0.1124 1.9509 0.1090 > 24373 24372 86.1 0.1124 1.8518 0.1090 > 24378 24375 99.7 0.1500 49.8084 0.1529 > 24377 24375 86.5 0.1471 16.9457 0.1090 > 24376 24375 87.1 0.1476 15.3512 0.1090 > 24392 24390 71.6 0.1338 0.2163 0.1335 > 24391 24390 72.8 0.1231 0.3302 0.1229 > 24394 24392 152.1 0.1450 0.1137 0.1449 > 24393 24392 121.6 0.1011 0.1883 0.1010 > 24414 24394 32.9 0.1523 0.1900 0.1522 > 24396 24394 33.8 0.1529 0.1910 0.1529 > 24395 24394 40.7 0.1090 0.1519 0.1090 > 24342 24340 133.3 0.1870 0.5324 0.1449 > 24350 24342 80.5 0.1906 0.6983 0.1522 > 24344 24342 85.5 0.2383 4.0017 0.1529 > 24343 24342 90.9 0.1423 0.6476 0.1090 > 24347 24344 104.1 0.2560 11.9267 0.1522 > 24346 24344 81.7 0.2082 3.4103 0.1090 > 24345 24344 82.9 0.1728 4.6679 0.1090 > 24354 24352 38.4 0.1465 0.1761 0.1449 > 24366 24354 54.4 0.1527 0.0985 0.1522 > 24063 24061 31.1 0.2181 0.1464 0.1335 > 24072 24063 30.6 0.1828 0.1463 0.1449 > 24068 24066 46.3 0.1202 0.1123 0.1090 > 24067 24066 44.6 0.1209 0.1131 0.1090 > 24070 24069 92.8 0.0417 0.1386 0.1090 > > step 0: Water molecule starting at atom 395505 can not be settled. > Check for bad contacts and/or reduce the timestep if appropriate. > wrote pdb files with previous and current coordinates step 0 > Warning: 1-4 interaction between 24378 and 24384 at distance 61.758 which > is larger than the 1-4 table size 2.000 nm These are ignored for the rest > of the simulation This usually means your system is exploding, if not, you > should increase table-extension in your mdp file or with user tables > increase the table size > ------------------------------------------------------ > Program mdrun, VERSION 4.5.3 > Source code file: pme.c, line: 534 > > Fatal error: > 5 particles communicated to PME node 2 are more than 2/3 times the cut-off > out of the domain decomposition cell of their charge group in dimension x. > This usually means that your system is not well equilibrated." > > > Thank You, > > regards, > Anu > > > > > On Tue, Feb 19, 2013 at 6:26 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > > > > > On 2/19/13 1:36 AM, Anu Chandran wrote: > > > >> Sir, > >> Thank you for the reply. As per the suggestion, I tried increasing > >> the rlist. Note or warning stopped when rlist was increased to 1.8. > >> Also with this value of rcoulomb, the box size also needs to be > >> increased. I would like to know whether it is fine to keep rlist 1.8 > >> and also whether there is any other alternative rather than > >> increasing rlist since increase in rlist requires an increase in box > >> size. > >> > > > > I would investigate why you have such large charge groups. For a > > protein in water (which is what you appear to have based on the .mdp > > file), you should not have such large charge groups. Haphazardly > > adjusting cutoffs can have a negative effect on the simulation. > > Increasing rlist may result in poorer performance. Why are you using > > a switching potential for van der Waals interactions? Exact > > specifications for OPLS are hard to come by in the literature, but most > commonly one sees: > > > > rvdw = 1.0 > > vdwtype = cutoff > > rlist = 1.0 > > rcoulomb = 1.0 > > coulombtype = PME > > > > -Justin > > > > > > Thank you, > >> with regards > >> Anu > >> > >> On Fri, Feb 15, 2013 at 5:28 PM, Dr. Vitaly Chaban > >> <vvcha...@gmail.com > >> >wrote: > >> > >> I am tyring to do a simulation of a monomer and an octamer of the > >> same > >>>> molecule > >>>> using gromacs 4.5.3 with opls force field. Monomer simulations ran > >>>> with > >>>> > >>> out > >>> > >>>> any note or > >>>> warning, but when i tried to do nvt equilibration for the octamer, > >>>> i got > >>>> > >>> the > >>> > >>>> following note while running grompp > >>>> > >>>> "NOTE 1 [file nvt.mdp]: > >>>> The sum of the two largest charge group radii (0.779095) is > >>>> larger than > >>>> rlist (1.400000) - rvdw (1.000000)" > >>>> The mdp file used is as follows: > >>>> > >>>> define = -DPOSRES > >>>> integrator = md > >>>> dt = 0.002 > >>>> nsteps = 50000 > >>>> nstcomm = 10 > >>>> nstxout = 100 > >>>> nstvout = 100 > >>>> nstlog = 100 > >>>> nstenergy = 100 > >>>> nstlist = 5 > >>>> ns_type = grid > >>>> pbc = xyz > >>>> rlist = 1.4 > >>>> coulombtype = PME > >>>> rcoulomb = 1.4 > >>>> epsilon_r = 1 > >>>> vdwtype = Switch > >>>> rvdw_switch = 0.9 > >>>> rvdw = 1.00 > >>>> fourierspacing = 0.12 > >>>> pme_order = 4 > >>>> ewald_rtol = 1e-5 > >>>> optimize_fft = yes > >>>> Tcoupl = nose_hoover > >>>> tc_grps = Protein Non-Protein > >>>> tau_t = 0.4 0.4 > >>>> ref_t = 300 300 > >>>> nh-chain-length = 1 > >>>> pcoupl = no > >>>> gen_vel = yes > >>>> gen_temp = 300.0 > >>>> gen_seed = 1984 > >>>> continuation = no > >>>> constraints = all-bonds > >>>> constraint-algorithm = LINCS > >>>> lincs-order = 4 > >>>> lincs-iter = 1 > >>>> lincs-warnangle = 30 > >>>> > >>>> > >>>> Can anybody please help me on how to go about with it? > >>>> > >>> > >>> > >>> 1) Increase RLIST > >>> 2) Re-distribute atoms among charge groups so that to make charge > >>> groups [spatially] smaller. > >>> > >>> > >>> > >>> Dr. Vitaly V. Chaban > >>> MEMPHYS - Center for Biomembrane Physics Department of Physics, > >>> Chemistry and Pharmacy University of Southern Denmark Campusvej 55, > >>> 5230 Odense M, Denmark > >>> -- > >>> gmx-users mailing list gmx-users@gromacs.org > >>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.g > >>> romacs.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? Read > >>> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.or > >>> g/Support/Mailing_Lists> > >>> > >>> > > -- > > ==============================**========== > > > > 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.gro > > macs.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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