On 9/28/12 8:53 AM, Gavin Melaugh wrote:
Hi
I have an alcohol system and I want to calculate the number of H bonds
during the trajectory.
My atom type labels are C2-C2-C2-CO-OH-HO. CO denotes carbon bonded to
oxygen, OH denotes alcohol oxygen, and HO denotes alcohol hydrogen.
In g_hbond how do I specify my groups to consider for H bonding. If I
uses group 0 which is the whole system it says that I have twice as many
acceptors as donors, which shouldn't be the case.
g_hbond uses atom names (not types) to determine what is considered a donor,
acceptor, or H atom. If there is a problem with the number of acceptors or
donors, then there is a problem with the way the atoms are named. Without
seeing the [atoms] section of the topology or relevant snippet of the coordinate
file, it's hard to say what's going on at this point.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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 gmx-users@gromacs.org
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 gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
