[gmx-users] so difficult problem
mohsen ramezanpour
ramezanpour.mohsen at gmail.com
Thu Jan 6 19:22:18 CET 2011
Dear Amit
I entered these commands for rotating box:
editconf -f conf.gro -o output.pdb -rotate 0 0 25.4
and then:
editconf -f output.pdb -o newbox.pdb -rotate 0 127.67548 0
as a result my molecul is located out of box totally,of course drug and
protein are bind to eachother yet.
thanks in advance for your attention and reply
On Tue, Jan 4, 2011 at 1:25 PM, Amit Choubey <kgp.amit at gmail.com> wrote:
> 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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