Re: minimizing bad system: bad global excl. count

From: Himanshu Khandelia (hkhandel_at_memphys.sdu.dk)
Date: Wed Jan 24 2007 - 05:53:51 CST

Hi,

I realized that the problem was because my topology for the lipid was
different than the once used by the membrane plugin.

Can anyone please advise me how to alter the membrane.tcl script to use it
from my own user-defined directory location ? I tried to make the
following changes in the section of the script where I thought the
directory locations were specified. But this did not work.

################
    # set package WD and files
    global env
    if ([info exists env(MEMBRANEDIR)]) {
# set psffile $env(MEMBRANEDIR)/${lipid}_box.psf
# set pdbfile $env(MEMBRANEDIR)/${lipid}_box.pdb
# set topfile $env(MEMBRANEDIR)/top_all27_prot_lipid.inp
       set pdbfile ~/${lipid}_box.pdb
       set psffile ~/${lipid}_box.psf
       set topfile ~/top_all27_prot_lipid.inp
    } else {
# set psffile [file normalize [file dirname [info script]]]/${lipid}_box.psf
# set pdbfile [file normalize [file dirname [info script]]]/${lipid}_box.pdb
# set topfile $env(MEMBRANEDIR)/top_all27_prot_lipid.inp
       set pdbfile ~/${lipid}_box.pdb
       set psffile ~/${lipid}_box.psf
       set topfile ~/top_all27_prot_lipid.inp
    }
    set tempfile temp
################

P.S: I was not able to modify the topology file or the membrane.tcl script
in its original location
(/usr/local/lib/vmd/plugins/noarch/tcl/membrane1.0/) because of permission
problems.

Thank you very much for the help,

-Himanshu

(I have also copied this message to the VMD list as it might be useful for
people in the future there)

On Tue, 23 Jan 2007, Brian Bennion wrote:

> 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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