Re: [AMBER] I can't visualize (in vmd) the output from an Accelerated MD (aMD) run

From: Jonathan Gough <jonathan.d.gough.gmail.com>
Date: Sun, 5 May 2013 12:20:37 -0400

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)
>
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Received on Sun May 05 2013 - 09:30:24 PDT
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