Hi Justin Thanks for the reply. To create a virtual site at the centre of geometry of 3 atoms, according to the manual, do you not say: [virtual_sitesn], the index of the site, the index of the three atoms and then the function type 1 which determines that it is COG. Or as I now realise. State [virtual_site3], site index atom indices, and function 1. The fact that there are no parameters then by default must mean it is COG. Is this correct?
Gavin Justin A. Lemkul wrote: > > > Gavin Melaugh wrote: >> Hi >> Having tried to run grompp using the data below I keep getting the >> following error >> Fatal error: >> Unknown vsiten type 7 >> Does anyone know why this might be? >> > > Your [virtual_sites] directive is not correct, either in its name (no > such thing as "virtual_sitesn" - the "n" should be replaced by a digit > indicating the type) or in the contents. See manual section 5.2.2. > > -Justin > >> Gavin >> >> Gavin Melaugh wrote: >>> Hi >>> >>> I am trying to alter a topology to include 3 virtual sites and I have a >>> few queries, the answers to which are not obvious form the manual. >>> Do I declare the virtual sites in the atomtypes directive like so >>> >>> ;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 >>> VS1 0.0 0.0 V >>> 0.0 0.0 >>> VS2 0.0 0.0 V >>> 0.0 0.0 >>> VS3 0.0 0.0 V >>> 0.0 0.0 >>> >>> Do I give them an index number in the atoms directive e.g. >>> >>> [atoms] >>> ; atomnr type resnr residue name cgnr charge mass >>> 1 CA 1 CGE CA 1 -0.1150 12.0110 >>> 2 CB 1 CGE CB 1 0.0000 12.0110 >>> 3 CA 1 CGE CA 2 -0.1150 12.0110 >>> 4 CB 1 CGE CB 2 0.0000 12.0110 >>> 5 CA 1 CGE CA 3 -0.1150 12.0110 >>> .......... >>> .......... >>> 229 VS1 2 VIR VS1 85 0.0000 0.0000 >>> 230 VS2 3 VIR VS2 86 0.0000 0.0000 >>> 231 VS3 4 VIR VS3 87 0.0000 0.0000 >>> >>> Then if I want to set up a virtual site between the COG of 3 atoms do I >>> do it in the following way >>> >>> [virtual_sitesn] >>> ;site COG of three hydrogens at window >>> ;site i j k func >>> 229 7 40 58 1 >>> 230 10 25 55 1 >>> 231 28 37 52 1 >>> >>> >>> Cheers >>> >>> Gavin >>> >>> >>> >>> Gavin Melaugh wrote: >>> >>>> Hi Sikandar >>>> >>>> A couple of questions regarding the virtual sites. >>>> 1) Do I have to number the virtual site in accordance with the atom >>>> indices of the rest of the molecule? >>>> 2) Is the parameters for the virtual site declared in the atomtypes >>>> directive? >>>> >>>> Cheers >>>> >>>> Gavin >>>> >>>> Sikandar Mashayak wrote: >>>> >>>>> in doing so .. by default all pair interactions with virtual sites >>>>> would result in zero forces except those between atoms defined in >>>>> [nonbond_params] >>>>> >>>>> On Thu, May 5, 2011 at 11:57 AM, Sikandar Mashayak >>>>> <symasha...@gmail.com <mailto:symasha...@gmail.com>> wrote: >>>>> >>>>> hey >>>>> >>>>> another approach to do this without using energy group exclusion >>>>> is to define non-bonded interactions parameter explicitly between >>>>> atoms in ffnonbonded.itp file. You can specify sigma and epsilon >>>>> to be zero in virtual sites atoms definition and specify >>>>> individual pair interactions parameters using non-bonded >>>>> interactions like following ... >>>>> >>>>> ; virtual site >>>>> VS1 0 0 0 D 0 0 >>>>> VS2 0 0 0 D >>>>> 0 0 >>>>> VS3 0 0 0 D 0 0 >>>>> >>>>> [ nonbond_params ] >>>>> VS1 C 1 1.0 0.25 >>>>> VS2 C 1 1.0 0.25 >>>>> VS2 C 1 1.0 0.25 >>>>> >>>>> -- >>>>> sikandar >>>>> >>>>> On Thu, May 5, 2011 at 11:47 AM, Gavin Melaugh >>>>> <gmelaug...@qub.ac.uk <mailto:gmelaug...@qub.ac.uk>> wrote: >>>>> >>>>> Hi Justin >>>>> >>>>> I do not intend to have charges on the sites. All I want is; >>>>> when a CH3 group gets close to the site it feels a repulsive >>>>> force. I >>>>> have calculated a sigma and epsilon value for this >>>>> interaction. >>>>> >>>>> Gavin >>>>> >>>>> Justin A. Lemkul wrote: >>>>> > >>>>> > >>>>> > Gavin Melaugh wrote: >>>>> >> Hi Justin >>>>> >> >>>>> >> I am reading the manual at the moment. I want to include >>>>> some virtual >>>>> >> sites in my molecule so that only surrounding CH3s atom >>>>> type C3 interact >>>>> >> with then. All other atoms I don't want to interact with >>>>> them. Do I >>>>> >> create energy groups in the index file called say "virtual >>>>> sites" and >>>>> >> "exclusions", and list all the indices of the atom types >>>>> that I don't >>>>> >> want to interact with the virtual site in one group and >>>>> all >>>>> the virtual >>>>> >> sites in another. >>>>> >> e.g >>>>> >> >>>>> >> [virtual sites] >>>>> >> 17 18 19 20 >>>>> >> >>>>> >> [virtsite_exclus] >>>>> >> 1 2 3 4 5 6 7 8 9 ..... >>>>> >> >>>>> > >>>>> > In a general sense, yes, that's the right approach. Note >>>>> that if any >>>>> > of these sites is charged and/or you're using PME, then >>>>> this >>>>> whole >>>>> > exclusion thing goes out the window, as has been discussed >>>>> several >>>>> > times in recent days. Using energygrp_excl applies only to >>>>> > short-range nonbonded interactions. If you need complete >>>>> exclusion, >>>>> > you may have to look into tabulated potentials if this is >>>>> the case. >>>>> > >>>>> > -Justin >>>>> > >>>>> >>>>> -- >>>>> gmx-users mailing list gmx-users@gromacs.org >>>>> <mailto: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 >>>>> <mailto: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! 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