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

Ricardo O. S. Soares ross_usp at yahoo.com.br
Sat May 19 20:42:32 CEST 2012 

I thank you all so much for aiding me on this matter, Jan, Peter and Justin. Now things are way clerarer!

Cheers,

Ricardo.




>________________________________
> De: Peter C. Lai <pcl at uab.edu>
>Para: jalemkul at vt.edu; Discussion list for GROMACS users <gmx-users at gromacs.org> 
>Enviadas: Sábado, 19 de Maio de 2012 1:01
>Assunto: Re: [gmx-users] Different Lipids into one Moleculetype (for position restrain)
> 
>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
>Programmer/Analyst        | KAUL 752A
>Genetics, Div. of Research    | 705 South 20th Street
>pcl at uab.edu            | Birmingham AL 35294-4461
>(205) 690-0808            |
>==================================================================
>
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