On Wed, Nov 4, 2009 at 20:41, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Ondrej Marsalek wrote: >> >> I thought that this was needed to convert the hydrogens to virtual >> sites, based on reading section 6.5 of the manual and some other >> things. Is this not correct? >> > > I don't believe constraining angles is necessary. The manual only refers to > fixed bond lengths. If you're looking for an example to follow, I would > suggest running the lysozyme benchmark described in the GROMACS 4 paper;
OK, so now I am mildly confused. I have downloaded the benchmarks pack (gmxbench-3.0.tar.gz) from the GMX website. The pme.mdp file for lysozyme indeed says "constraints = all-bonds". On the other hand, the topology contains virtual sites in the list of atoms, but there are no [virtual_site?] sections. And the timestep is 4 fs. Could someone please help me clarify this? Thanks, Ondrej > the > parameters used are nicely detailed. I got reasonable results using > "constraints = all-bonds," but if that is not correct, perhaps someone else > can comment. > > -Justin > >> Ondrej >> >> >> On Wed, Nov 4, 2009 at 20:07, Justin A. Lemkul <jalem...@vt.edu> wrote: >>> >>> Ondrej Marsalek wrote: >>>> >>>> Dear GROMACS users, >>>> >>>> I would like to substitute hydrogens in a protein with virtual sites >>>> to allow for the 4-5 fs timestep mentioned in the GROMACS 4 paper and >>>> several other places. So far, I have not found an example or a >>>> tutorial that would involve this, so I want to create a >>>> straightforward example. I have taken the 2KO3 structure from the PDB >>>> and went through this sequence of commands: >>>> >>>> pdb2gmx -v -f 2KO3.pdb -o initial-vacuum.gro -ff oplsaa -water tip4p >>>> -vsite hydrogens -ignh >>>> editconf -f initial-vacuum.gro -o initial-box.gro -c -d 1 -bt cubic >>>> genbox -cp initial-box.gro -cs tip4p.gro -p topol.top -o conf.gro >>>> grompp >>>> >>>> I also provided a pretty standard grompp.mdp, that contains >>>> "constraints = h-angles". I get the following error: >>>> >>>> ------------------------------------------------------- >>>> Program grompp, VERSION 4.0.5 >>>> Source code file: vsite_parm.c, line: 779 >>>> >>>> Fatal error: >>>> Automatic parameter generation not supported for Virtual site 3 atom 4 >>>> for this bonding configuration >>>> ------------------------------------------------------- >>>> >>>> I am not sure what the problem is. I would appreciate and help on the >>>> use of this feature, pointers to resources, or a working example. >>>> Reading the manual and searching did not help as much as I would like. >>>> >>> Have you tried specifying either "all-bonds" or "h-bonds" for >>> constraints? >>> I think "all-bonds" is the most commonly-used option. Any specific >>> reason >>> for using "h-angles"? >>> >>> -Justin >>> >>>> Thanks, >>>> Ondrej >>>> _______________________________________________ >>>> gmx-users mailing list gmx-us...@gromacs.org >>>> http://lists.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 >>> Ph.D. Candidate >>> ICTAS Doctoral Scholar >>> 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-us...@gromacs.org >>> http://lists.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 > Ph.D. Candidate > ICTAS Doctoral Scholar > 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-us...@gromacs.org > http://lists.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 > _______________________________________________ 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/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