Re: Re: how to use ethanol as solvent in namd for MD simulations?

From: Jian Liu (bay__gulf618_at_sina.com)
Date: Fri Jul 31 2009 - 07:33:35 CDT

Hi all,
I think VMD can deal with it perfectly,
and the full way is discussed in
http://www.mdbbs.org/thread-16499-1-1.html (Chinese).

VegaZZ is not compatible with VMD/NAMD well,
there is a bug (maybe) in VegaZZ's psf/pdb file in
http://www.mdbbs.org/thread-13166-1-1.html (Chinese),
I am not sure weather VegaZZ can generate the psf/pdb file with
proper atom name and atom type which are readable by NAMD

sincerely
Jian Liu

----- 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




  

Hi Wang,


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.


Branko


Wang Yf wrote:

  

dear all,
      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!
  sincerely,

wang.
  


  
  没有广告的终身免费邮箱,
www.yeah.net
  
  

No virus found in this incoming message.
Checked by AVG - www.avg.com
Version: 8.5.392 / Virus Database: 270.13.38/2274 - Release Date: 07/31/09 05:58:00

  


This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:22:16 CST