[gmx-users] Editing of the existing system

[James Starlight]

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>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?


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)
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

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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