Justin Cheers, I had just posted a more general query prior to you getting back? It is perhaps not as vague.
Gavin Justin A. Lemkul wrote: > > > Gavin Melaugh wrote: >> Hi Justin >> >> I Did the following and it worked. You were right about using one atom >> types directive. If you don't mind I have another query. In all my >> topology files to date (one molecule type), I have always listed the >> atomtypes in the [atomtypes] directive, and used the set up in >> [defaults] below. Is this all that is required for the calculation of >> the LJ energies. I have never used a pair list, a pair types directive >> or a nonbond_params directive. From the output I still get LJ energies >> but I am slightly confused by all the different options. >> > > I can't give a better explanation than what is already in the manual, > specifically section 5.3.3 ([nonbond_params] and whether or not you > need it). Whether or not you need [pairs] depends on the underlying > mechanics of the force field you're using. See section 5.3.5. > > -Justin > >> parameter level >> [defaults] >> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ >> 1 3 yes 0.5 0.5 >> >> [atomtypes] >> ;type mass charge ptype sigma(nm) >> epsilon(kjmol-1) >> CB 12.011000 0.000000 A 0.355000 0.292880 >> CA 12.011000 -0.115000 A 0.355000 0.292880 >> HC 1.008000 0.115000 A 0.242000 0.125520 >> CU 13.019000 0.265000 A 0.350000 0.334720 >> NU 14.007000 -0.597000 A 0.325000 0.711280 >> CH 13.019000 0.332000 A 0.385000 0.334720 >> C3 15.035000 0.000000 A 0.390500 0.732200 >> CT 12.011000 -0.180000 A 0.350000 0.276144 >> HH 1.008000 0.060000 A 0.250000 0.125520 >> >> #include "tertpentane.itp" >> #include "methylcage.itp" >> >> ;System level >> [system] >> ;the name of this system >> cage and pentane >> >> [molecules] >> ; moleculename number >> tertpentane 1 >> methylcage 1 >> >> >> Justin A. Lemkul wrote: >>> >>> Gavin Melaugh wrote: >>>> Hi Justin >>>> >>>> Cheers. I have attached my pentane itp file. The cage itp is formatted >>>> the same. In the examples there never seems to be [atom types] >>>> included. >>>> I have included it. Does it seem O.K? >>>> >>> You only need to use an [atomtypes] directive if you're introducing >>> new atom types into the force field. I don't know if it's >>> necessary. I also don't know if these sections can be discontinuous >>> (i.e., one >>> section present in cage.itp, another in tertpentane.itp). Try the >>> approach I sent you and see. If you get fatal errors, then you may >>> have to assemble a single [atomtypes] directive and put it either in >>> the first .itp file you #include, or before any of the #includes in >>> the .top (since #include really just means "cut-and-paste the stuff >>> here," it works the same). >>> >>> -Justin >>> >>>> Gavin >>>> >>>> Justin A. Lemkul wrote: >>>>> Gavin Melaugh wrote: >>>>>> Hi Mark. >>>>>> >>>>>> I have looked this up, but I am a little uncertain. Does one of the >>>>>> topologies have to be included within the other as an .itp file. >>>>>> If so >>>>> No. You #include .itp files to simply add molecules within a >>>>> .top; it >>>>> would be very rare to #include an .itp within an .itp (although it >>>>> can >>>>> be done). For your case, your .top is simple: >>>>> >>>>> #include (force field) >>>>> >>>>> #include "cage.itp" >>>>> #include "pentane.itp" >>>>> >>>>> [ system ] >>>>> My system >>>>> >>>>> [ molecules ] >>>>> Cage 1 >>>>> Pentane 1 >>>>> >>>>>> do I only define the [defaults directive] in the .top file i.e. I >>>>>> take >>>>>> it I don't include this directive in the .itp file as well. >>>>>> >>>>> The [defaults] directive is provided by whatever force field you >>>>> #include. If you're using some custom parameters, then it needs >>>>> to be >>>>> defined once (and only once) at the top of your .top file. >>>>> Otherwise, >>>>> you'll get fatal errors from grompp. >>>>> >>>>> -Justin >>>>> >>>>>> Cheers >>>>>> >>>>>> Gavin >>>>>> >>>>>> Mark Abraham wrote: >>>>>>> Look up the include file mechanism on the webpage. >>>>>>> >>>>>>> Mark >>>>>>> >>>>>>> ----- Original Message ----- >>>>>>> From: Gavin Melaugh <gmelaug...@qub.ac.uk> >>>>>>> Date: Tuesday, September 28, 2010 19:04 >>>>>>> Subject: [gmx-users] topology file for two molecules >>>>>>> To: Discussion list for GROMACS users <gmx-users@gromacs.org> >>>>>>> >>>>>>>> Hi all >>>>>>>> >>>>>>>> I want to run a simulation of one tert-pentane molecule inside one >>>>>>>> organic cage molecule. I have the topology files for both >>>>>>>> molecules but >>>>>>>> obviously I only need one .top file as the input for grompp. >>>>>>>> What is the >>>>>>>> most convenient way of having both topologies in one file? >>>>>>>> >>>>>>>> Many Thanks >>>>>>>> >>>>>>>> Gavin >>>>>>>> -- >>>>>>>> gmx-users mailing list gmx-users@gromacs.org >>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>>>>>> Please search the archive at >>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists >> >> > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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