From: Jian Liu (bay__gulf618_at_sina.com)
Date: Fri Jul 31 2009 - 07:33:35 CDT
I think VMD can deal with it perfectly,
and the full way is discussed in
VegaZZ is not compatible with VMD/NAMD well,
there is a bug (maybe) in VegaZZ's psf/pdb file in
I am not sure weather VegaZZ can generate the psf/pdb file with
proper atom name and atom type which are readable by NAMD
----- Original Message -----
From: Branko <bdrakuli_at_chem.bg.ac.yu>
To: Wang Yf <yunfenwang126_at_126.com>, namd-l_at_ks.uiuc.edu
Subject: Re: namd-l: how to use ethanol as solvent in namd for MD simulations?
Date: 2009-7-31 17:50:17
Try to use VegaZZ (free software @
http://www.ddl.unimi.it/vega/download.htm) to build cluster and prepare
your input. Vega can be used as NAMD (2.6 and 2.7b1) GUI and offer
user-friendly solvent cluster builder, as well as solvation tool.
Wang Yf wrote:
how to use ethanol as solvent in namd for MD simulations ?
could anyone can describe it in detail for me ?
thanks a lot in advance!
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