[gmx-users] so difficult problem
Amit Choubey
kgp.amit at gmail.com
Tue Jan 4 10:26:30 CET 2011
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.mohsen at 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.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
>>
>
>
> --
> 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/20110104/15ae7656/attachment.html>
More information about the gromacs.org_gmx-users
mailing list