From: Brian Bennion (bennion1_at_llnl.gov)
Date: Tue Jan 23 2007 - 14:35:19 CST
Hello,
Can you post your pdf and psf files? It might be that the psf file
as an extra bond between to very distant atoms. Viewing the pdb file
with VMD will not find this kind of error. I assume that viewing the
psf and pdb together doesn't lead to any weirdness?
Brian
At 09:32 AM 1/23/2007, Himanshu Khandelia wrote:
>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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