Thanks for the corrections. I had to mock up parts of it because usually I only POSRE_RECEPTOR and POSRE_LIGAND. I also have a mix of putting the position restraints in .itp file vs. in the topol.top, depending on how often I am changing my topol.top (things like genion and g_membed modify them).
On 2012-05-18 11:00:55PM -0400, Justin A. Lemkul wrote: > > > On 5/18/12 10:28 PM, Peter C. Lai wrote: > > Synopsis: position restraints are coupled to the moleculetype. So you need > > to > > define position restraints individually for each molecule type contiguous > > with their topologies. > > > > There's a couple of ways to do it, using some simple #include and #define: > > > > You can restrain within each molecule's own .itp file at the end, for > > example: > > > > popc.itp: > > [ moleculetype ] > > ; Name nrexcl > > POPC 3 > > > > [ atoms ] > > ; nr type resnr residue atom cgnr charge mass > > typeB... > > ; residue 1 POPC rtp POPC q 0.0 > > 1 NTL 1 POPC N 1 -0.6 14.007 .... > > ... > > 20 PL 1 POPC P 20 1.5 30.974 .... > > ... > > > > [ dihedrals ] > > ... > > ; end of original file > > > > #ifdef POSRE_LIPID > > [ position_restraints ] > > ; atom type fx fy fz > > 20 1 1000 1000 1000 > > ;restrain atom 20 in the molecule_type which is P > > #endif > > > > Add something similar at the bottom of pope.itp. > > > > Then in your system-wide topol.top would look something like: > > > > #include "charmm36.ff/forcefield.itp" ;charmm36 lipids > > > > #include "popc.itp" > > #include "pope.itp" > > > > #include "charmm36.ff/tips3p.itp" ;charmm waters > > > > [ system ] > > POPC+POPE bilayer > > > > [ molecules ] > > POPC 100 > > POPE 100 > > SOL 10000 > > ; or however many of each you have in your conf.gro file > > > > In your grompp.mdp, you'd have: > > > > #define -DPOSRE_LIPID ; to turn on position restraints in lipid .itps > > > > ------------------------------ > > > > Another way to do it is to put the #ifdef POSRE_LIPID [ position_restraints > > ] > > sections in the system-wide topol.top, but you'd need two of them, one per > > lipid [ moleculetype ]: > > > > #include "charmm36.ff/forcefield.itp" ;charmm36 lipids > > > > #include "popc.itp" > > #ifdef POSRE_LIPID > > [ position_restraints ] ;for POPC > > 20 1 1000 1000 1000 > > #endif > > > > #include "pope.itp" > > #ifdef POSRE_LIPID > > [ position_restraints ] ;for POPE > > ... > > #endif > > ... > > > > The grompp.mdp file would continue to use #define -DPOSRE_LIPID to enable > > those restraints. > > > > It is up to you how you want to modularize the restraints. You can even > > use multiple #defines to restrain separately (although the resulting system > > wouldn't necessarily be physically correct): > > > > As above topologies but: > > > > #ifdef -DPOSRE_POPC > > ;position restraints for POPC > > #endif > > > > I think what you mean here is: > > #ifdef POSRE_POPC > > > #ifdef -DPOSRE_POPE > > ;position restraints for POPE > > #endif > > > > and #ifdef POSRE_POPE. > > Otherwise, the define statement becomes very cumbersome (and perhaps faulty), > with: > > define = -D-DPOSRE_POPC -D-DPOSRE_POPE > > > and in grompp.mdp: > > > > #define -DPOSRE_POPC -DPOSRE_POPE > > ;to restrain both > > > > Note that for the .mdp, one does not use #define, but rather: > > define = -POSRE_POPC -DPOSRE_POPE > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > 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 [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street [email protected] | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
