[gmx-users] NPT

[Justin A. Lemkul]

mohsen ramezanpour wrote:
> On 1/3/11, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>
>> mohsen ramezanpour wrote:
>>> Dear All
>>> In doing umbrella sampling ,when I want to generate NPT every thing is
>>> going well but one error is occuring in the first.
>>> please let me know how can  I solve this problem.
>>> Is it usefull to extend the degree which is defined in .mdp file?
>> No.  The constraints are failing, but they are not the problem that needs to
>> be
>> fixed.  Please see:
>>
>> http://www.gromacs.org/Documentation/Terminology/Blowing_Up
>> Dear Justin
> I looked at that page,I changed timestep to 0.001 and even to 0.0005
> but it did not have any positive effect,I think the .mdp file in
> umbrella sampling page is not proper in my problem(protein-ligand
> docking),what do you think?

If you're taking it directly from the tutorial, it may need some tweaking to 
suit your needs.  But if your system is failing immediately (step 0), it is far 
more likely that there is a physical instability that cannot be avoided by 
simply changing the time step.  Please see the "Diagnosing an Unstable System" 
section on that page.  It contains basically all the advice that one normally 
gets in this situation.

-Justin

> thanks in advance
>> -Justin
>>
>>> 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'
>>> 50000 steps,    100.0 ps.
>>>
>>> Step 0, time 0 (ps)  LINCS WARNING
>>> relative constraint deviation after LINCS:
>>> rms 1504.051113, max 55378.273438 (between atoms 5289 and 5290)
>>> bonds that rotated more than 30 degrees:
>>>  atom 1 atom 2  angle  previous, current, constraint length
>>>    5264   5263   40.6    0.1143   0.1260      0.1140
>>>    5293   5294   82.7    0.1221 2613.7048      0.1090
>>>    5291   5293   77.2    0.1517 6084.3052      0.1390
>>>    5291   5292  101.0    0.1117 1519.0425      0.1090
>>>    5289   5291   87.7    0.1353 6893.7969      0.1390
>>>    5289   5290   88.4    0.1437 7531.5815      0.1360
>>>    5289   5287   88.4    0.1456 7542.5801      0.1390
>>>    5287   5288   89.7    0.1092 381.6111      0.1090
>>>    5285   5287   92.3    0.1395 355.0215      0.1390
>>>    5285   5286  123.8    0.1101  44.8588      0.1090
>>>    5284   5293   89.0    0.1478 4606.4570      0.1390
>>>    5284   5285   79.3    0.1402 173.6082      0.1390
>>>    5278   5279   78.9    0.1529   1.1246      0.1530
>>>    5277   5278  122.9    0.1545  13.1470      0.1530
>>>    5276   5284   84.9    0.1422 159.0514      0.1390
>>>    5276   5277   68.4    0.1543  90.8518      0.1530
>>>    5276   5275   39.5    0.1439  72.5391      0.1430
>>>    5274   5275  103.7    0.1436  21.6098      0.1430
>>>    5273   5274  108.6    0.1394   3.3410      0.1390
>>>    5276   5272   45.7    0.1402  80.7004      0.1390
>>>    5272   5273  127.3    0.1340  14.2414      0.1330
>>>    5272   5270   69.8    0.1336  12.6282      0.1330
>>>    5270   5271  113.3    0.1092   0.2532      0.1090
>>>    5268   5270  104.5    0.1391   0.2727      0.1390
>>>    5268   5269   44.0    0.1091   0.1624      0.1090
>>>    5273   5266   58.5    0.1342  14.0148      0.1330
>>>    5265   5268   36.7    0.1394   0.1774      0.1390
>>>
>>> Actually md is crush,of course I think so.
>>> Thanks in advance
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
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> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================