[gmx-users] Different Lipids into one Moleculetype (for position restrain)

[Peter C. Lai]

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
> 
> ========================================
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Peter C. Lai			| University of Alabama-Birmingham
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