[gmx-users] links warnangles

[Justin A. Lemkul]

Justin A. Lemkul wrote:
> 
> 
> vferrario at units.it wrote:
>> No, is not working also in this case... probably the problem is with 
>> my mdp files:
>>
> 
> I would argue that it's the coordinates that are the problem.  For 
> instance, compare the distances expected by the topology:
> 
>     1     3     1     0.1758
>     1     4     1     0.1758
>     1     5     1     0.1758
>     2     3     1     0.233839
>     2     4     1     0.233839
>     2     5     1     0.233839
>     3     4     1     0.290283
>     3     5     1     0.290283
>     4     5     1     0.290283
> 
> with the actual distances found in the coordinate file:
> 
>     1     3     1     0.177
>     1     4     1     0.177
>     1     5     1     0.174
>     2     3     1     0.240
>     2     4     1     0.235
>     2     5     1     0.235
>     3     4     1     0.282
>     3     5     1     0.290
>     4     5     1     0.289
> 
> The model requires 9 constraints to be satisfied in harmony.  If the 
> starting geometry isn't perfect (or very close to it), there's probably 
> too much rearranging required to make the model work.  Removal of the 
> explicit H probably yielded a set of constraints that could be somewhat 
> satisfied by EM, but fall apart in MD, which could be for a variety of 
> reasons.
> 

I've obtained a stable trajectory for a single CHCL3 molecule.  By setting 
"continuation = no" (so that constraints are not solved before step 0) in the 
em.mdp file, and then reducing nstlist to 5 in md.mdp, I was able to run 100 ps 
of MD with no issue.  The value of nstlist is probably the cause of the crash 
you mention.  Updating the neighborlist every 200 fs is 10-20 times too long.

-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

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