On 2/14/18 9:42 AM, Justin Lemkul wrote:
On 2/14/18 9:33 AM, Easton J.W. wrote:
Thanks Justin,
Will this effect the interactions (both bonded and non-bonded) that
these atoms have, as their atom types are not in the forcefield itp
files?
Missing atom types would cause grompp to fail; you'd never get to the
point where a simulation would be affected.
You're introducing custom atom types in the topology itself, and
that's always legal before any [moleculetype] appears. The LJ
parameters come from the [atomtypes] directive. Masses and charges
present in that directive aren't used.
Actually, to clarify: *if* masses are present in the [atoms] directive
of a [moleculetype], then the masses found in [atomtypes] are not used.
Strictly speaking, it is not necessary to have explicit masses in
[atoms], though nearly all topologies do.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
==================================================
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
