Re: Using CHARMM-GUI membrane builder with NAMD

From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Mon Aug 02 2010 - 02:37:09 CDT

On Friday 30 July 2010 16:17:36 Ajasja Ljubetič wrote:
> Dear NAMD users,
>
> does anyone have any experiance using the files generated with CHARMM-GUI
> membrane builder in NAMD? The xplor psf and the pdb files are of course not
> a problem, but the input files for the equilibration (which consists of 6
> steps) would need a lot of work to translate to NAMD configurations files.
> Has anybody done this already?
>
> For example I know there is the keep_water_out.tcl script (which has been
> giving me problems during the kcsa tuturial, but I can't remember the
> details now), but the same could be achieved using tcl boundary forces, or
> the grid forces or perhaps simply by first fixing (or constraining) the
> water molecules.
>
>
> Best regards,
> Ajasja

Why not simply use constraints like charmm does and reduce the scaling factor.

Something like this:

#Use VMD to set the BETA vaule to the desired constraint
#(make sure all other BETA values are 0)
#% set cons [atomselect top "protein"]
#% $cons set beta 10
#% set sel [atomselect top all]
#% $sel writepdb k.pdb

constraints on
consref k.pdb
conskfile k.pdb
conskcol B
constraintScaling 1.0
#############################################################
## EXECUTION SCRIPT
##
#############################################################

# Minimization
minimize 20000 ;#
reinitvels $temp ;#

#500000 = 10ns
run 20000
constraintScaling 0.5
run 20000
constraintScaling 0.2
run 20000
constraintScaling 0.1
run 20000
constraintScaling 0.05
run 20000
constraintScaling 0
run 380000

I don't know, if you can switch between the consref/conskfile file in a single
run or if you have to start anoter run if you want to include/exclude other
Atoms in your consref/conskfile.

Cheers
Bjoern

-- 
Bjoern Olausson
Martin-Luther-Universität Halle-Wittenberg 
Fachbereich Biochemie/Biotechnologie
Kurt-Mothes-Str. 3
06120 Halle/Saale
Phone: +49-345-55-24942

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