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 <[email protected]> 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 <[email protected] >> >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 [email protected] >>> 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 [email protected]. >>> * Can't post? Read >>> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/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 [email protected] > 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 [email protected]. > * Can't post? 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