thanks Dan, I really appreciate it!
On Sun, May 5, 2013 at 12:05 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Sun, May 5, 2013 at 6:46 AM, Jonathan Gough
> <jonathan.d.gough.gmail.com> wrote:
> > ntb=2, cut=12.0, ntp=1,igb=0,ntwprt = 3381,ioutfm = 1,
>
> Is there any particular reason you are setting ntwprt? If your system
> has more than 3381 atoms this will result in you generating a
> trajectory that has a different # of atoms than your topology. Unless
> you have a topology that matches your trajectory (i.e. one that is set
> up for 3381 atoms) you cannot view it in VMD. You can use parmed or
> cpptraj to generate a corresponding topology. However, unless space is
> really a concern it's probably better to not set ntwprt at all.
>
> -Dan
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun May 05 2013 - 09:30:24 PDT
