If I create an .rtp file for my molecule how can I use this file when I producing gro and top files and Can I use this .rtp file with oplsaa and gromos 96 force fields for two different md run successfuly ? Because I plan to run md simulations for all atom and united atom force fields and compare the results. Secondly If I use PRODRG , the only force field I can use is oplsaa. Is it true ? Can't I use a gromos 96 force field ?
--- 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: "Gromacs Users' List" <[email protected]> Date: Wednesday, March 11, 2009, 9:53 PM Adrien Delmont wrote: > 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. > Most (if not all) of the parameters you will need will already be present in the force field. No modification of any of these files should be necessary.. If you want to use pdb2gmx to create your topology, you need to create an .rtp entry. For a simple alkane (especially with a UA representation), it should be trivial to write the topology by hand with a text editor and a thorough understanding of Chapter 5. Alternate ideas: 1. Use PRODRG to generate a rough topology. Verify its contents before proceeding, make any modifications you need, and validate the resulting topology. 2. Don't use Gromos96. AFAIK, none of the Gromos variants deal very well with hydrocarbon chains. OPLS might be better, but I think there are some limitations there, too. -Justin > --- 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 > > ======================================== > > -- ======================================== 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 ======================================== _______________________________________________ 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
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