Good evening, 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 (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme_old/index.html) 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. [email protected] -- 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 [email protected].
