[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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