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 <kgp.a...@gmail.com> 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 < > ramezanpour.moh...@gmail.com> 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 <kgp.a...@gmail.com> 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 < >>> ramezanpour.moh...@gmail.com> 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 gmx-users@gromacs.org >>>> 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 gmx-users-requ...@gromacs.org. >>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>> >>> >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> 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 gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >> >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> 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 gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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