May be you broke the molecule while using editconf. Try to fix the periodicity by trjconv and then use it.
On Tue, Jan 4, 2011 at 1:14 AM, mohsen ramezanpour < [email protected]> wrote: > 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 >> > > > -- > 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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