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 <jalem...@vt.edu
<mailto:jalem...@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
--
========================================
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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