From: Joshua D. Moore (jdmoore_at_unity.ncsu.edu)
Date: Thu Jan 19 2006 - 21:30:12 CST
Hi,
The NBfix command may be useful for this, but I never tested to see if it
was implemented still or not. It was used in NAMD v 1.5. See my post
from before. I will email you separately the page from NAMD v 1.5 that
describes this.
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/2747.html
There is also VDW_PAIRS. I am not sure what they are, but it seems to
also sound like it would be related. I think that someone must know
because I think some people are using it.
Josh
On Thu, January 19, 2006 8:06 pm, Hyonseok Hwang wrote:
> Dear all,
>
> I know that the standard format of adding new LJ parameters in NAMD is :
>
> atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4
> !
> C 0.000000 -0.110000 2.000000 ! ALLOW PEP POL ARO
>
> My question is whether there is another format of adding LJ parameters
> like this in NAMD:
>
> atom1 atom2 epsilon Rmin
> C1 C2 -0.123 3.000
> C1 H1 -0.012 2.500
>
> I suppose that this is similar to the way of adding LJ parameters in
> GROMACS.
>
> If anybody knows something about this, please let me know.
> Thanks a lot in advance.
>
> -Hyon
>
>
--------------------------------------------------
Joshua D. Moore
Graduate Student
North Carolina State University
Department 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
--------------------------------------------------
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:41:33 CST