[gmx-users] so difficult problem

[mohsen ramezanpour]

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













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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