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?
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! 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