I generated my .top and .gro file as drug/enzyme tutorial. I used PRODRG to generate them. I could pass all of steps in UMbrella sampling tutorial with these files,without any warning or error. the one thing I changed is rotating box with editconf.
On Tue, Jan 4, 2011 at 12:38 PM, Amit Choubey <[email protected]> wrote: > There is something wrong with your initial configuration. May be you forgot > to take care of periodicity, how did you get your initial configuration? > Also notice that these kind of problems have been discussed previously. > > Amit > > On Tue, Jan 4, 2011 at 12:33 AM, mohsen ramezanpour < > [email protected]> wrote: > >> Dear All >> I am using this .mdp file and I recived the below warnings,I can't solve >> that. >> >> >> title = NPT >> define = >> integrator = md >> tinit = 0 >> dt = 0.002 >> nsteps = 500000 >> nstcomm = 1 >> comm-grps = protein non-protein >> niter = 20 >> nstxout = 5000 >> nstvout = 5000 >> nstfout = 0 >> nstlog = 5000 >> nstenergy = 250 >> nstxtcout = 250 >> xtc-precision = 1000 >> xtc_grps = protein non-protein >> energygrps = Protein non-protein >> nstlist = 5 >> ns_type = grid >> pbc = xyz >> rlist = 1.4 >> domain-decomposition = no >> coulombtype = PME >> rcoulomb-switch = 0 >> rcoulomb = 1.4 >> epsilon-r = 1 >> vdw-type = Cut-off >> rvdw-switch = 0 >> rvdw = 1.4 >> DispCorr = EnerPres >> fourierspacing = 0.12 >> fourier_nx = 0 >> fourier_ny = 0 >> fourier_nz = 0 >> pme_order = 4 >> ewald_rtol = 1e-05 >> epsilon_surface = 0 >> optimize_fft = no >> tcoupl = Nose-hoover >> tc-grps = Protein non-protein >> tau_t = 0.1 0.1 >> ref_t = 300 300 >> Pcoupl = Parrinello-Rahman >> Pcoupltype = Isotropic >> tau_p = 1.0 >> compressibility = 4.5e-5 >> ref_p = 1.0 >> annealing = no >> gen_vel = yes >> gen_temp = 310 >> gen_seed = 173529 >> constraints = all-bonds >> constraint-algorithm = Lincs >> unconstrained-start = no >> lincs-order = 4 >> lincs-warnangle = 30 >> morse = no >> >> my sytem is protein-ligand,I want to generate a NPT. >> the result was: >> >> Step 0, time 0 (ps) LINCS WARNING >> relative constraint deviation after LINCS: >> rms 0.002537, max 0.119994 (between atoms 5293 and 5294) >> bonds that rotated more than 30 degrees: >> atom 1 atom 2 angle previous, current, constraint length >> starting mdrun 'Protein in water' >> 500000 steps, 1000.0 ps. >> >> Step 0, time 0 (ps) LINCS WARNING >> relative constraint deviation after LINCS: >> rms 1503.633433, max 55362.878906 (between atoms 5289 and 5290) >> bonds that rotated more than 30 degrees: >> atom 1 atom 2 angle previous, current, constraint length >> 5264 5263 41.7 0.1143 0.1261 0.1140 >> 5293 5294 82.7 0.1221 2612.9744 0.1090 >> 5291 5293 77.2 0.1517 6082.6147 0.1390 >> 5291 5292 101.0 0.1117 1518.6106 0.1090 >> 5289 5291 87.7 0.1353 6891.8911 0.1390 >> 5289 5290 88.4 0.1437 7529.4878 0.1360 >> 5289 5287 88.4 0.1456 7540.4873 0.1390 >> 5287 5288 89.7 0.1092 381.5114 0.1090 >> 5285 5287 92.3 0.1395 354.9220 0.1390 >> 5285 5286 123.8 0.1101 44.8448 0.1090 >> 5284 5293 89.0 0.1478 4605.1763 0.1390 >> 5284 5285 79.3 0.1402 173.5627 0.1390 >> 5278 5279 78.9 0.1529 1.1270 0.1530 >> 5277 5278 122.9 0.1545 13.1423 0.1530 >> 5276 5284 84.9 0.1422 159.0098 0.1390 >> 5276 5277 68.4 0.1543 90.8248 0.1530 >> 5276 5275 39.5 0.1439 72.5216 0.1430 >> 5274 5275 103.7 0.1436 21.6028 0.1430 >> 5273 5274 108.5 0.1394 3.3421 0.1390 >> 5276 5272 45.7 0.1402 80.6795 0.1390 >> 5272 5273 127.3 0.1340 14.2401 0.1330 >> 5272 5270 69.8 0.1336 12.6250 0.1330 >> 5270 5271 113.3 0.1092 0.2530 0.1090 >> 5268 5270 104.6 0.1391 0.2718 0.1390 >> 5268 5269 44.4 0.1091 0.1636 0.1090 >> 5273 5266 58.5 0.1342 14.0125 0.1330 >> 5265 5268 36.5 0.1394 0.1769 0.1390 >> >> Back Off! I just backed up step0b.pdb to ./#step0b.pdb.2# >> >> Back Off! I just backed up step0c.pdb to ./#step0c.pdb.2# >> Wrote pdb files with previous and current coordinates >> step 0Warning: 1-4 interaction between 5264 and 5273 at distance 13.965 >> which is larger than the 1-4 table size 2.400 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 >> >> Please let me know the solution. >> Thanks in advance >> >> >> >> >> >> >> -- >> gmx-users mailing list [email protected] >> 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 [email protected]. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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