Thanks again for your reply.
In the previous mail you suggest to use rstwt = -1.0, 1.0; can I use another value for the same. The -1 and 1 indicates that simple difference of two separation, if I use 2.0 then it will be difference of double separation. Am I right?
I think by using (x_2 - x_1) you indicate the separation between atom1 and atom2. But in the input I have to specify r1, r2, r3, r4; which is the difference of separation, but what will be the value of individual separation?
Actually, in my case one H-atom is bonded with one N-atom and during the reaction the H-atom will shift towards another O-atom. I want to increase the N-H bond length and decrease H-O separation and set the reaction coordinate as the difference of two separation. So my doubt is that if I specify the r1, r2... (difference of separation) then two separation with change simultaneously, or it will change only one.
It is not clear to me what is the difference in sander and pmemd?
With best regards
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 9:11 AM
Subject: Re: [AMBER] How to define reaction coordinate in Umbrella sampeling
On Fri, Jun 28, 2013 at 10:19 PM, Sindrila Dutta banik <sindrila.duttabanik.yahoo.com> wrote:
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?
>
According to Section 6.1.1 of the Amber 11 manual, the rstwt variable is used to signify that a particular restraint defined by 4 atoms is either a torsion or generalized distance coordinate of 2 distances. If you set rstwt to a non-zero value, then the code will correctly treat the 4-atom coordinate as a linear combination of 2 distances. If you do not set rstwt, then your restraint will be interpreted as a torsion restraint.
Examples:
Torsion restraint
&rst
iat=1,2,3,4, rk2=5.0, rk3=5.0, r1=-100, r2=0, r3=0, r4=100
/
LCOD of 2 distances
&rst
iat=1,2,3,4, rk2=5.0, rk3=5.0, r1=-10, r2=0, r3=0, r4=10, rstwt=-1.0,1.0,
/
The latter input file will create a reaction coordinate that is -1*(x_2 - x_1) + 1*(x_4 - x_3).
>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"?
>
Both will work. The first one is not really supported anymore, so if you run into problems you will likely have to debug them yourself (and figure out how to use it yourself). The first one does not require nmropt=1. The second one (which has more support), does require nmropt=1.
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 - 23:00:02 PDT
