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.
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. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists