[gmx-users] Editing of the existing system

[Justin A. Lemkul]

James Starlight wrote:
> Justin,
> 
> I've minimised my system to emtool=1.0
> but the error still occurs
> 
> 
> 31 марта 2012 г. 16:27 пользователь Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> написал:
> 
> 
>     Separate COM motion removal groups are tricky.  I'm still not
>     completely clear on what your system looks like, but if you've got
>     two proteins in two layers of solvent and you expect one or both of
>     them to move in such a way that they begin to interact, it may not
>     be appropriate to be using the groups you've shown below.
> 
> 
>  My system consist of membrane receptor in membrane-like bilayer 
> surrounded by water. Also part of the receptor is in the water layer. To 
> this part wich are in the water another water-soluble protein ( part of 
> the G-protein) has been attached.
> 
>  
> 
>     And what was the exact outcome?
> 

Please note I was asking for the exact outcome of EM, not the crashing MD.  What 
I wanted to see was the magnitude of the potential energy and maximum force, as 
directly copied and pasted from your screen/log output.

> 
> This is the error log
> 
> Getting Loaded...
> Reading file nvt.tpr, VERSION 4.5.4 (single precision)
> Loaded with Money
> 
> 
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.002373, max 0.102422 (between atoms 1387 and 1388)

Start by inspecting the initial configuration in the vicinity of these atoms. 
Something is likely clashing here.

> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
> starting mdrun 'B2ar_in_Ccl4 in water'
> 500000 steps,   1000.0 ps.
> 
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 73.552702, max 3051.386475 (between atoms 8551 and 8552)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>    1407   1412   34.8    0.1530   0.1955      0.1530
>    1407   1408   35.2    0.1530   0.1943      0.1530
>    1405   1407  152.5    0.1471   0.1638      0.1470
>    1405   1406  123.6    0.1001   0.2394      0.1000
> etc - the above- part of atoms of the first protein
> 
> 
>    8519   8520   44.3    0.1001   0.1498      0.1000
>    8517   8519   41.6    0.1331   0.1901      0.1330
>    8478   8480   54.9    0.1330   0.1555      0.1330
>    8478   8479   44.8    0.1230   0.1262      0.1230
>    8465   8478   52.7    0.1530   0.1491      0.1530
> this is part of atoms of the second protein
> 
> 
> Also I've attached my nvt.mdp file
> 

I am still not clear why you have set the COM motion removal groups as you have. 
     For a pure biphasic system, it can be appropriate to remove COM motion in 
the two layers separately, as they can slide with respect to one another.  If 
you have proteins that may partition between the layers, this goes out the 
window, as the COM motion removal may actually fight against the underlying 
physics.  To test, set "comm-grps = System."

-Justin

> in this file
>  a_1-4232 is the first protein
>  a_8365-8643 is the second protein.
> 
> 
> What's wrong with this system?
> 
> James
> 
> 
>  

-- 
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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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