[gmx-users] so difficult problem
mohsen ramezanpour
ramezanpour.mohsen at gmail.com
Tue Jan 4 10:14:15 CET 2011
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.amit at 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.mohsen at 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 at 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-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
> --
> gmx-users mailing list gmx-users at 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110104/303db3c7/attachment.html>
More information about the gromacs.org_gmx-users
mailing list