Question regarding reverse CG to all-atom

From: parikshit moitra (prkshtmoitra_at_gmail.com)
Date: Tue Jan 21 2014 - 04:42:04 CST

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.

This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:22:03 CST