[gmx-users] How to Search Forums and Creating Binary from Existing Topology/Trajectory File
rwmolt07 at gmail.com
Fri Mar 11 23:17:39 CET 2016
I have two questions, one general, one specific.
The big question is that I do not understand how to search the GROMACS
forums efficiently. The search bar on
(http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List) allows a
search to be conducted, but the links shown do not seem to be of the
user forums and are very slow to load when selected. I can see the grand
list of all messages on
(https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/) but it's
not clear to me how to search it for a particular string.
The specific reason I wanted to search the forums was to answer a very
specific question. I may as well pose it here, as well. I have converted
an Amber trajectory into the GROMACS form; I have also converted an
Amber parameter file to a GROMACS form. I would like to create a GROMACS
binary (tpr file).
1.) From what I have gleamed from tutorials, I need to use a variant of
the pdb2gmx command (presumably not for a pdb, but for a trajectory)?
2.) I also do not wish to use the methods of various tutorials like
in terms of loading an existing force field; the parameters I have were
developed in-house. I thus would like to load my
converted-from-Amber-to-Gromacs topology file. Instead of the -ff flag,
what flag indicates use of an existing parameter file?
3.) An important caveat: I have to use the 4.5 version of Gromacs. I
hope the commands are all the same, since I know the current version of
Gromacs is 5.0
Thank you for your time
Dr. Robert Molt Jr.
r.molt.chemical.physics at gmail.com
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