On 1/13/13 1:57 PM, learnmd wrote:
Hello,
I am new to gromacs and I hope I can get help with a problem. I want to add
a heavy water model to gromacs and then run simulations with a box full of
that solvent. I know the parameters (the O-D) bond length, bond angles and
LJ parameters for the system.
How do I make an .itp file for this system? Will Gromacs recognize D as
Write it in a text editor after a thorough read through Chapter 5 of the manual.
You can edit an existing file (like spc.itp) if you want a template. If
you're introducing new atomtypes and other parameters, you will need additional
directives (again, consult Chapter 5).
Deuterium and still count it as hydrogen bond or should I just use H in the
There's nothing during run time that cares about hydrogen bonds. The g_hbond
program determines putative hydrogen bonds by reading atom names. In that case,
using the name "H" is useful, but a topology can be hacked afterwards to use
whatever atom names you like.
model to avoid such confusion. Also, how do I make an initial coordinate
file and then a box of solvent (like the spc216.gro) provided in the
installation.
genbox -ci -nmol or simply use spc216.gro and equilibrate thoroughly, as is done
with other 3-point models.
-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
========================================
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