AW: Question regarding reverse CG to all-atom

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Jan 21 2014 - 06:18:10 CST

Hi,

 

please notice that a one-by-one conversion from CG to all-atom is not
possible. Therefore it is likely and expected that the resulting model is
pretty bad. In some unlucky cases, it is also expected, that especially side
chain atoms can be superimposed. So you might want to have a look at your
structure about superimposed atoms, means very close contacts which should
be easy to figure out with the "dynamic bonds" representation, varying the
cutoff value or by using tcl. You can correct the structure manually in VMD
using "Mouse->Move->Atom" and drag the atoms off each other. A careful
minimization will be necessary afterwards in any case and you might like to
use some restraints for the backbone angles during it.

 

Good luck

 

Norman Geist.

 

Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von parikshit moitra
Gesendet: Dienstag, 21. Januar 2014 11:42
An: namd-l_at_ks.uiuc.edu; owner-namd-l-digest_at_ks.uiuc.edu;
namd-l-digest_at_ks.uiuc.edu
Betreff: namd-l: Question regarding reverse CG to all-atom

 

Hello all,

I am doing Martini Coarse Graining simulation by NAMD. But after completion
of the production run, when I am converting the final structure from
coarse-grain to all-atom mode, the structure of the final molecule is very
erroneous. I thought that this may be a normal case for CG simulation.

Then I tried doing simulated annealing after all-atom minimization run. But
always I found the vanderwaal's energy to be very expensive in each case and
for this the simulated annealing step failed. I ran the minimization at 0.1
fs/step, but even then similar results obtained. I have pasted the VDW
energy output below:

 

ETITLE: TS BOND ANGLE DIHED IMPRP
ELECT VDW BOUNDARY MISC KINETIC
TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG
PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG

 

ENERGY: 500 9486888.6339 2252253.5111 85281.6395 72257.0677
288734.2756 -9999999999.9999 0.0000 0.0000 0.0000
-9999999999.9999 0.0000 -9999999999.9999 -9999999999.9999
0.0000 -9999999999.9999 -9999999999.9999 7662267.7184
-9999999999.9999 -9999999999.9999

I shall be grateful if someone can show me a wayout from this.

- Thanks,

  Parikshit Moitra.

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