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 - 21:00:02 PDT
