----- Forwarded Message -----
From: Yao Yao <yao0o.ymail.com>
To: Jason Swails <jason.swails.gmail.com>
Sent: Friday, October 7, 2011 5:12 PM
Subject: Re: [AMBER] Gromacs Make Index in AMBER
make_ndx can choose specific atoms, groups or residues and make an index file for them,
when calculating the energy or analyze the trajectory (rms, correlation, hbond ....), it can only calculate the properties of the indexed part alone if you include the index file when issuing commands.
________________________________
From: Jason Swails <jason.swails.gmail.com>
To: Yao Yao <yao0o.ymail.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Friday, October 7, 2011 5:00 PM
Subject: Re: [AMBER] Gromacs Make Index in AMBER
Unlikely. What does make_ndx do exactly?
On Fri, Oct 7, 2011 at 6:56 PM, Yao Yao <yao0o.ymail.com> wrote:
Hi,
>
>In gromacs I often use make_ndx command to pick specific atoms, groups or residues of my interest
>for energy calculation purpose or so on. Does AMBER has similar command or flag I can use?
>
>Thanks,
>
>Yao
>_______________________________________________
>AMBER mailing list
>AMBER.ambermd.org
>http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Oct 07 2011 - 17:30:03 PDT
