Nilesh Dhumal wrote:
By default, Within a same molecule 1-2 and 1-3 interactions does it get
excluded?
If nrexcl > 2, yes. The default (pdb2gmx) behavior sets nrexcl=3, but you
haven't indicated how you generated your topology.
-Justin
Nilesh
On Tue, November 9, 2010 10:19 am, Justin A. Lemkul wrote:
Nilesh Dhumal wrote:
Hello,
I am working on a system which has a diatomic solute surrounded by water
molecules. I want to exclude the 1-2 and 1-3 interactions for solute. I
am using OPLS force fild (Gromacs version 4.0.5).
If it's diatomic, what 1-3 interactions can it have? Set nrexcl in the
topology accordingly. That's what it's there for.
-Justin
Nilesh
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected]. Can't post? Read
http://www.gromacs.org/Support/Mailing_Lists
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
