[ 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
Sorry to bother you so much times. Above is the real parameter I used in my top file which probably specified the dihedrals as periodic (function 1) . But I also used OPLS force field which should read different parameters as RB. So when the MD runs, does it just read this parameters in the periodic dihedrals as a RB parameter? If my top is in a wrong form, how can md runs well and give a good result? 2009/1/28 Justin A. Lemkul <jalem...@vt.edu>: > > > Yanmei Song wrote: >> >> 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? >> > > Well, the numbers in the .top for the dihedrals were designed to be > components of a periodic dihedral (function type 1 in the .top), which is > not of the same form as an R-B dihedral (function type 3). My guess would > be that the parameters you have specified are not appropriate for use 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! >> > > I suppose you would have OPLS UA, as far as your atom types are concerned. > I don't know for sure, I've never used the UA version of OPLS. If you want > the .top for your own molecule, you may have to write it by hand, perhaps > even using the PRODRG topology as a skeleton (along with a thorough > understanding of Chapter 5 of the manual, as Mark advised). Depending on > the size of your molecule, this manual process may be a chore, so you could > also consider making an entry for your molecule within ffoplsaa.rtp. Make > a local copy in the working directory to ensure that you don't break > something by accident! > > -Justin > >> 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 >>> >> >> >> > > -- > ======================================== > > 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