AW: problem in solvating a graphene layer created using VMD-nanotube builder

From: Norman Geist (
Date: Tue Mar 05 2013 - 00:18:44 CST

Hi Sridhar,


first of all this is a VMD question, not a NAMD question. You are supposed
to get the best answers for VMD question in the VMD mailing list, as most
people ignore them here.


Additionally, you didn’t say what the error actually is, to say only that
the script isn’t working, doesn’t point out a lot IMHO.


Norman Geist.


Von: [] Im Auftrag
von Sridhar Kumar Kannam
Gesendet: Dienstag, 5. März 2013 04:37
Betreff: namd-l: problem in solvating a graphene layer created using
VMD-nanotube builder


Hi Fellow researchers,


I have created a graphene layer using VMD nanotube builder I am getting a
strange problem when I am trying to solvate it.


My very simple script is below ...



graphene -lx 20 -ly 20 -type zigzag -nlayers 1 -b 1 -a 0 -d 0 # creates a
graphene layer

set all [atomselect top all]

$all set segname X

$all writepsf graphene.psf

$all writepdb graphene.pdb

solvate graphene.psf graphene.pdb -z 5 +z 5 -o solvate



The above script is working fine when my graphene dimentions are below 15
and 15 which will have less than 10000 carbon atoms.

for example with this line the script is working fine - graphene -lx 15 -ly
15 -type zigzag -nlayers 1 -b 1 -a 0 -d 0


So I thought the problem could be due to more than 10000 residues (nanotube
builder is giving a new residue id to each carbon atoms)

I set all the carbon atoms residues to "1" by using the command - $all set
resid 1 - before writing the above psf and pdb files...

But it did not help ...


Can anyone please give me a clue ....




Cheers !!!
Sridhar  Kumar Kannam :)

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