[gmx-users] so difficult problem

Wed Jan 12 11:23:11 CET 2011

Hi Mohsen,

You're doing something terribly wrong. But why you want to do what you
attempt eludes me. Maybe it helps if you give an explanation of what
you want, in stead of what doesn't work. In addition, give the set of
commands that bring you up to this point, and not only the output of
mdrun. That way we can probably see where you go astray.

Cheers,

Tsjerk

On Wed, Jan 12, 2011 at 10:55 AM, mohsen ramezanpour
<ramezanpour.mohsen at gmail.com> wrote:
>
> Dear Dr.Tsjerk
>
> Before doing md for generating NPT, I did an EM,the result was:
> poteintial energy:-2.2611160*10^(6)
> Max F=4.8960352*10^(4) on atom 5289
> Besides I had done EM before on the same system,I just add solvent by genbox
> and Ions by genion.
> the above result is for Energy minimization after adding ions by genion.
>
> I did what you said.but when I was generating NPT equilibration
> I recieved this massage:
>
>
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 8.387059, max 321.381958 (between atoms 5289 and 5290)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>    5293   5294   74.4    0.1137  12.9330      0.1090
>    5291   5293   59.1    0.1422  32.1605      0.1390
>    5291   5292  103.5    0.1096   9.8747      0.1090
>    5289   5291   89.5    0.1383  39.2022      0.1390
>    5289   5290   85.7    0.1410  43.8439      0.1360
>    5289   5287   85.4    0.1426  44.0196      0.1390
>    5287   5288   90.2    0.1091   1.5178      0.1090
>    5285   5287   88.7    0.1391   1.9186      0.1390
>    5285   5286   41.8    0.1092   0.1322      0.1090
>    5284   5293   87.2    0.1429  21.7425      0.1390
>    5284   5285   92.4    0.1393   2.0880      0.1390
>    5277   5278   79.1    0.1532   0.5213      0.1530
>    5276   5284   63.0    0.1394   1.8946      0.1390
>    5276   5277   79.2    0.1534   0.7278      0.1530
>    5276   5275   79.9    0.1432   0.6036      0.1430
>    5274   5275   82.0    0.1431   0.3189      0.1430
>    5276   5272   82.1    0.1393   0.6113      0.1390
>    5272   5273   74.2    0.1333   0.2251      0.1330
>    5272   5270   77.7    0.1332   0.2428      0.1330
>    5270   5271   46.5    0.1091   0.1682      0.1090
>    5268   5270   36.9    0.1391   0.1854      0.1390
>    5273   5266   41.4    0.1334   0.1933      0.1330
> Wrote pdb files with previous and current coordinates
> step 0Warning: 1-4 interaction between 5272 and 5293 at distance 22.443
> 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 what can I do.
> thanks in advance
>
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> On Thu, Jan 6, 2011 at 11:20 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
>>
>> Hi Mohsen,
>>
>> I think rotating a molecule with editconf will not rotate the box. Then
>> again, if it did, it would result in a box violating Gromacs requirements.
>> Either way, it's not going to work like that. Build a new box after
>> rotation... And have a good look at what you're actually trying now by
>> taking the rotated system and stack it a few times using genconf -nbox 2 2 2
>>
>> Cheers,
>>
>> Tsjerk
>>
>> On Jan 6, 2011 7:22 PM, "mohsen ramezanpour"
>> <ramezanpour.mohsen at gmail.com> wrote:
>>
>> 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 e...
>>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands