[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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