What makes me so confused is that I used this top for the MD run using ffoplsaa.itp and the there are no error message. Also I got a good result compared to experiment. Does it mean that what I did is totally wrong with using this top in combination with OPLS?
Also if I used the atom type in opls_x with the x is less than 135, then it should be OPLS UA force field right? if I want to use OPLS, How can we get the top? Thank you so much for your help! 2009/1/28 Justin A. Lemkul <jalem...@vt.edu>: > > > Yanmei Song wrote: >> >> Hi,Justin: >> >> Thanks for your response. >> >> I have read that part and still confused. Does it mean that if I >> choose the ffoplsaa.itp in my top, I used the RB potential for >> Dihedrals or the periodic type? Also actually I can only get the >> parameters for phi, cp and mult (listed above) Can I use these >> parameters directly for my itp user ffoplsaa force field? Thanks a >> lot! >> > > OPLS does use the R-B potential. It looks like that topology is a PRODRG > product, in which case, no, your topology is not suitable for use with OPLS. > PRODRG generates Gromos-type topologies. > > -Justin > >> 2009/1/28 Justin A. Lemkul <jalem...@vt.edu>: >>> >>> Yanmei Song wrote: >>>> >>>> Hi, >>>> >>>> I am using ffoplsaa.itp as my force field to do a simulation using >>>> GROMACS. >>>> I have a question about how to write the parameters in dihedrals in >>>> the itp file. >>>> >>>> [ dihedrals ] >>>> ; ai aj ak al fu c0, c1, m, ... >>>> 1 2 5 6 1 0.0 3.77 3 0.0 3.77 3 ; dih CAA >>>> CBF OAW CBH >>>> 2 5 6 9 1 0.0 3.77 3 0.0 3.77 3 ; dih CBF >>>> OAW CBH OAY >>>> 5 6 9 10 1 0.0 3.77 3 0.0 3.77 3 ; dih OAW >>>> CBH OAY CBJ >>>> 6 9 10 13 1 0.0 3.77 3 0.0 3.77 3 ; dih CBH >>>> OAY CBJ OBA >>>> 9 10 13 14 1 0.0 3.77 3 0.0 3.77 3 ; dih OAY >>>> CBJ OBA CBL >>>> >>>> Then if I am choosing ffoplsaa.itp force field, what is the meaning >>>> for c0,c1 and m under the [dihedrals]? Since i know that GROMOS and >>>> OPLS force field have a different format for proper dihedrals. For >>>> OPLS it seems there are four other parameter like v1 v2 v3 v4. Then my >>>> question is how can i define the dihedral parameters in itp file based >>>> on ffoplsaa force field in GROMACS? Thanks a lot! >>>> >>> Refer to the manual, section 4.2.12 "Proper Dihedrals." >>> >>> -Justin >>> >>>> Yanmei >>> >>> -- >>> ======================================== >>> >>> Justin A. Lemkul >>> Graduate Research Assistant >>> 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 gmx-users@gromacs.org >>> 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 gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >> >> >> > > -- > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > 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 gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Yanmei Song Department of Chemical Engineering ASU _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
