[gmx-users] Editing of the existing system

James Starlight jmsstarlight at gmail.com
Mon Apr 2 16:28:51 CEST 2012

By the way

Today I've examined in vacuum minimisation outputs more carefully (
watching in vmd trr ) and found that conformation of the loops in the
docked regions were changed after long CG minimisation.

Then I've resolvate my system and add ions and run STEEP minimisation of
that system.

After this I've decreasing integration step to the from 0.001 to 0.0001.

Unfortunatelly the error was the same

starting with the LINK warnings like

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.002089, max 0.082711 (between atoms 1387 and 1388)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

and ending with the exploiding of my system as well with the eror like

step 29: Water molecule starting at atom 42310 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates

Also I've changed COM groups ( to the System value in one case as well as
placing the second protein group to the common group with the first protein
and membrane in the second case ). But the result was the same.

Is there any  suggestions or should I start with another conformation of
first protein ?


2 апреля 2012 г. 9:56 пользователь James Starlight
<jmsstarlight at gmail.com>написал:

> Justin,
> Thanks again for attention to my problem.
> I've checked my system and found that the problem was exactly in the 1388
> atom ( wich is not properly minimized in accordance to the log files). This
> atom is the Cb atom of Gln residue wich placed between one loop of the
> protein and docked alpha helix of the peptide. The  surrounding of that
> atom ( It's likely that other intracellular loops of the receptor as well
> as long N term protect this side chain to rotate during the minimisation ).
> When I've checked pdb files produced by exploding system I've found that
> some atoms ( from that loops) were moved from the pereodic boundaries (
> I've obtain very big system as the conseqyence surrounding by some single
> atoms. So it all look like as big artifact :) )
> So it seems that I need to use slightly different initial conformation of
> the receptor because minimisation could not to resolve such crushes.
> Thanks again
> James
> 1 апреля 2012 г. 21:37 пользователь Justin A. Lemkul <jalemkul at vt.edu>написал:
>> James Starlight wrote:
>>> Justin,
>>> Sorry again for the delay.
>>> I've finished minimise my system with the CG algorithm in double
>>> precision ( after steep minimisation )
>>> but the output was
>>> Stepsize too small, or no change in energy.
>>> Converged to machine precision,
>>> but not to the requested precision Fmax < 0.1
>>> Than I've tried to equilibrate this system with the NVT conditions and
>>> obtain old error about collapse of my system :)
>>>  I've found logs of both minimisation ( the step minimisation log was
>>> very big I've coppied only end part of this output data )  and attach it to
>>> this topic.
>> Both of these log files indicate that EM was likely fine.  For future
>> reference, the following sections were all I was asking for all along:
>> From CG:
>> Potential Energy  = -5.96597537065782e+05
>> Maximum force     =  1.42815783701700e+02 on atom 1388
>> Norm of force     =  1.58963638409829e+00
>> From steep:
>> Potential Energy  = -5.7233788e+05
>> Maximum force     =  7.0209003e+02 on atom 1388
>> Norm of force     =  1.1310696e+01
>> CG gives you the better minimization, overall, as expected.  Atom 1388
>> bears the maximum force, but it is not of problematic magnitude.
>>  Also I've run minimisation in vacuum as you've told me but this results
>>> would be aviable tomorrow.
>> It's probably not necessary, after all.  I was guessing at that point
>> based on incomplete information.
>>  Could you tell me whats exactly wrong with that system and is there
>>> possible ways to fix the problem?
>> As I've said before, the only strange thing you seem to be doing is with
>> your comm-grps.  Change this setting to "System" and see if it runs.
>>  Otherwise, I can find no reason for the immediate instability.  If it
>> still crashes, perhaps decrease the time step for the initial equilibration.
>> -Justin
>> --
>> ==============================**==========
>> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>> ==============================**==========
>> --
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