[gmx-users] so difficult problem
Amit Choubey
kgp.amit at gmail.com
Tue Jan 4 10:55:57 CET 2011
Could you post the exact command lines ?
On Tue, Jan 4, 2011 at 1:38 AM, mohsen ramezanpour <
ramezanpour.mohsen at gmail.com> 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 <kgp.amit at 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.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
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
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>>>>
>>>>
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