--- On Wed, 3/11/09, Adrien Delmont <[email protected]> wrote:
From: Adrien Delmont <[email protected]> Subject: Re: [gmx-users] get a box of 100 molecules To: [email protected] Date: Wednesday, March 11, 2009, 9:46 PM The molecule I use is a simple hydrocarbon ( n-heptane ) and I think that I should add something like dihedral, bond, angle parameters after I search the literature. I found some information about that. I think I will add parameters into the related force fields .itp file. Is it true ? And then I will create a box of 100 molecules without any error. --- On Wed, 3/11/09, Justin A. Lemkul <[email protected]> wrote: From: Justin A. Lemkul <[email protected]> Subject: Re: [gmx-users] get a box of 100 molecules To: [email protected], "Discussion list for GROMACS users" <[email protected]> Date: Wednesday, March 11, 2009, 9:11 PM Adrien Delmont wrote: > I just want to add missing parameters for my molecule in order to get ...gro and top files for example GROMOS96 43a2 force field . How can I add missing parameters ? I didn't find any information about this procedure. I'm waiting for your help. > You'll have to define what you mean by "parameters" - is this some new small molecule that has not been parameterized under this force field? Are you starting from scratch? If so, this is not a trivial problem for a beginner. Read here: http://wiki.gromacs.org/index.php/Parameterization If you have adequate parameters for most of your molecule and are missing something like a dihedral, etc. then read the primary literature and derive it yourself. This process is also complicated, but is probably less work than coming up with parameters for a brand new molecule. -Justin > Thanks in advance > > > --- On *Wed, 3/11/09, Mark Abraham /<[email protected]>/* wrote: > > From: Mark Abraham <[email protected]> > Subject: Re: [gmx-users] get a box of 100 molecules > To: "Discussion list for GROMACS users" <[email protected]> > Date: Wednesday, March 11, 2009, 4:58 PM > > Adrien Delmont wrote: > > > > ------------------------------------------------------------------------ > > *From:* Adrien Delmont <[email protected]> > > *To:* [email protected] > > *Sent:* Wednesday, March 11, 2009 6:09:53 PM > > *Subject:* Re: [gmx-users] get a box of 100 molecules > > > I didn't get gro and top files with any force field in Gromacs. I > basicly want to use oplsaa and GROMOS96 43a2 force field (improved alkane > dihedrals) . I think I should add all the parameters but how can I add my > parametes both into oplsaa and GROMOS96 43a2 force field ? > > You can't just mix force fields. See > http://wiki.gromacs.org/index.php/force_field > > Mark > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ======================================== Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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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