Re: vmd-l: namd2.7b1, tip4p, and dummies

From: Joshua D. Moore (jdmoore_at_unity.ncsu.edu)
Date: Wed Sep 30 2009 - 05:24:34 CDT

Dear Ed,
I haven't used it yet myself, but TIP4P seems to be available in the CVS
version and maybe the beta version of 2.7b1.

Here are two threads which give some information

http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/9807.html

http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/7288.html

It seems you should contact Peter Freddolino as he has some examples.

Probably you are going to get some comments about sending this to the VMD
list. I've copied the NAMD list, as I am sure others are interested on the
progress of this implementation.

Best.

Josh
<http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/9807.html>
------------------------------------------------
Joshua D. Moore
Graduate Student
North Carolina State University
Dept. of Chemical and Biomolecular Engineering
Box 7905 Centennial Campus
Engineering Building I
911 Partners Way
Raleigh, NC 27695-7905
Phone: (919) 513-2051
Fax: (919) 513-2470
Email: jdmoore_at_unity.ncsu.edu
------------------------------------------------

On Wed, Sep 30, 2009 at 2:36 AM, Edward Lyman <edward.lyman_at_gmail.com>wrote:

> Hi all,
>
> I have heard it said that namd can simulate 4 site water (tip4p, eg), and
> even read in gromacs formatted topology. But in the manual under the gromacs
> heading, it is mentioned that dummy atoms are not supported.
>
> Does this refer only to gromacs formatted inputs? ie, namd2.7b1 supports
> dummy atoms, just not via gromacs inputs? And if this is the case, where
> else might I find a parameter file, namd ready, of tip4p/2005 ?
>
> Thx,
> Ed
>
>

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