Re: [gmx-users] Trouble running simulations with Nitrogen
On 7/19/18 11:54 PM, Joshua Cummings wrote: Hi Everyone, I'm currently trying to run some simulations that involve the absorption of N2 into a liquid solvent. I'm having some difficulty in generating the topology for N2. For reference, the pdb file I have for N2 is as follows: HETATM1 N6B HDZ 0 0.000 0.000 0.553 1.00 0.00 N HETATM2 N6A HDZ 0 0.000 0.000 -0.553 1.00 0.00 N CONECT12 CONECT21 END When I try to generate the .itp file and topology via pdb2gmx (OPLS), gromacs doesn't recognise the residue. I've tried using both the LigParGen server and the PRODRG to generate the topology, but neither work. PRODRG generates an error saying it does not deal with mono/di-atomic molecules and LigParGen won't recognise N2 at all. I haven't had any trouble generating topologies for other small gas molecules such as CH4, am I missing something here or are OPLS parameters not possible for N2? Should I use some other forcefield for N2? There should be parameters in the literature for N2, perhaps not for OPLS-AA (the "L" is for "liquid," after all, and focuses on biomolecules and analogs) but might give you a place to start. In principle, the parametrization is pretty straightforward. The charges are zero, the bond length and vibrational frequency can be easily computed via QM if not determined experimentally via spectroscopy, and then you need to fit the LJ parameters to reproduce either liquid density/RDF at low temperature, free energy of solvation (if known), etc. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Trouble running simulations with Nitrogen
Hi Try this http://erg.biophys.msu.ru/tpp/ Best On Thu, Jul 19, 2018 at 10:54 PM, Joshua Cummings < joshua.cummi...@uon.edu.au> wrote: > Hi Everyone, > > > I'm currently trying to run some simulations that involve the absorption > of N2 into a liquid solvent. I'm having some difficulty in generating the > topology for N2. For reference, the pdb file I have for N2 is as follows: > > > HETATM1 N6B HDZ 0 0.000 0.000 0.553 1.00 0.00 >N > HETATM2 N6A HDZ 0 0.000 0.000 -0.553 1.00 0.00 >N > CONECT12 > CONECT21 > END > > > When I try to generate the .itp file and topology via pdb2gmx (OPLS), > gromacs doesn't recognise the residue. I've tried using both the LigParGen > server and the PRODRG to generate the topology, but neither work. PRODRG > generates an error saying it does not deal with mono/di-atomic molecules > and LigParGen won't recognise N2 at all. > > > I haven't had any trouble generating topologies for other small gas > molecules such as CH4, am I missing something here or are OPLS parameters > not possible for N2? Should I use some other forcefield for N2? > > > Thanks in advance everyone, > > > JOSHUA Cummings > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Trouble running simulations with Nitrogen
Hi Everyone, I'm currently trying to run some simulations that involve the absorption of N2 into a liquid solvent. I'm having some difficulty in generating the topology for N2. For reference, the pdb file I have for N2 is as follows: HETATM1 N6B HDZ 0 0.000 0.000 0.553 1.00 0.00 N HETATM2 N6A HDZ 0 0.000 0.000 -0.553 1.00 0.00 N CONECT12 CONECT21 END When I try to generate the .itp file and topology via pdb2gmx (OPLS), gromacs doesn't recognise the residue. I've tried using both the LigParGen server and the PRODRG to generate the topology, but neither work. PRODRG generates an error saying it does not deal with mono/di-atomic molecules and LigParGen won't recognise N2 at all. I haven't had any trouble generating topologies for other small gas molecules such as CH4, am I missing something here or are OPLS parameters not possible for N2? Should I use some other forcefield for N2? Thanks in advance everyone, JOSHUA Cummings -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.