[gmx-users] so difficult problem
mohsen ramezanpour
ramezanpour.mohsen at gmail.com
Tue Jan 4 10:38:16 CET 2011
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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>
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