minimizing bad system: bad global excl. count

From: Himanshu Khandelia (hkhandel_at_memphys.sdu.dk)
Date: Tue Jan 23 2007 - 11:32:41 CST

Hi,

I built a membrane using the membrane module and then solvated it using
solvate. The final system therefore has a lot of overlaps in the lipids,
and also has a thin (~ 1 A) vaccum slice between the water generated by
solvate and the water obtained from using the membrane module. When I
tried to minimize the system in NAMD, I got the bad global exclusion count
error.

The initial energy is obviously very high. As per earlier discussions on
the list, I tried each of the following, but nothing worked:

- increasing/decreasing periodic cell dimensions
- increasing/decreasing cutoffs
- with/without rattle
- checked lipid and water parameters, all is ok
- looked at the pdb in vmd, there are no extra-long bonds

Can anyone suggest anything else that might work ? The config file is
attached, and part of the output is below

Thank you very much

###################
Warning: Bad global exclusion count, possible error!
Warning: Increasing cutoff during minimization may avoid this.
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY MISC
KINETIC TOTAL

ENERGY: 0 99999999.9999 99999999.9999 99999999.9999
60.0134 39664966.2394 99999999.9999 0.0000 0.0000
0.0000 99999999.9999

OPENING EXTENDED SYSTEM TRAJECTORY FILE
TCL: Minimizing for 2000 steps
Warning: Bad global exclusion count, possible error!
Warning: Increasing cutoff during minimization may avoid this.
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY MISC
KINETIC TOTAL

ENERGY: 0 99999999.9999 99999999.9999 99999999.9999
60.0134 39664966.2394 99999999.9999 0.0000 0.0000
0.0000 99999999.9999

INITIAL STEP: 1e-06
GRADIENT TOLERANCE: nan
BRACKET: 0 nan nan nan nan
RESTARTING CONJUGATE GRADIENT ALGORITHM
..
..
..
################################################

----------------------------
Himanshu Khandelia
Research Assistant Professor (Postdoc)
MEMPHYS, Center for Membrane Physics
University of Southern Denmark (SDU)
Odense M 5230, Denmark
www.memphys.sdu.dk
Phone: +4565503510
email: hkhandel_at_memphys.sdu.dk
-----------------------------


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