How could I understand that my restrain is considered as LCOD and not any torsion. What is the difference in "sander" program and "pmemd" program. In the tutorial of umbrella sampling they use $AMBERHOME/bin/pmemd.MPI to run the job of umbrella sampling. Can I use the sander for the same?
In amber11 manual LCOD define in two sections namely Section 4.7.2. (122p) and Section 6.1.1. (177p). Here I use the second one. Is both is applicable for umbrella sampling? How to use the first one? For the first one shall I have to use "nmropt = 1"?
Thanks in advance.
Sindrila
________________________________
From: Jason Swails <jason.swails.gmail.com>
To: Sindrila Dutta banik <sindrila.duttabanik.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Saturday, 29 June 2013 1:54 AM
Subject: Re: [AMBER] How to define reaction coordinate in Umbrella sampeling
On Fri, Jun 28, 2013 at 3:35 PM, Sindrila Dutta banik <
sindrila.duttabanik.yahoo.com> wrote:
> thanks for the reply.
>
>
> So I have to use sander command to run the umbrella sampling. Is my input
> correct for combination of distance?
>
Not the one you posted. You need to add the rstwt=-1.0,1.0, to have it
recognized as a LCOD. Otherwise, as you pointed out, it's simply treated
as a torsion restraint.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Jun 28 2013 - 19:30:02 PDT
