Could you post the exact command lines ? On Tue, Jan 4, 2011 at 1:38 AM, mohsen ramezanpour < [email protected]> wrote:
> please let me know more. > I am new with gromacs. > did I understand correctly?You say me to use from trjconv at first and then > from editconf? > I want to keep fix my molecule and rotate my box to locate in awanted > direction. > waht can I do? > because when I rotate the box my molecule totally is located out of box,but > protein and ligand are connected as the first state and I think my molecule > has not broken. > Thanks in advance > > > On Tue, Jan 4, 2011 at 12:56 PM, Amit Choubey <[email protected]> wrote: > >> 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 >>> >> >> >> -- >> 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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