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

Peter C. Lai pcl at uab.edu
Sat May 19 04:28:07 CEST 2012

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:

[ 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

[ position_restraints ]
; atom  type      fx      fy      fz
     20     1  1000  1000  1000
;restrain atom 20 in the molecule_type which is P

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"
[ position_restraints ] ;for POPC
     20     1  1000  1000  1000

#include "pope.itp"
[ position_restraints ] ;for POPE

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:

;position restraints for POPC

;position restraints for POPE

and in grompp.mdp:

;to restrain both


#define -DPOSRE_POPC
; to restrain only POPC

On 2012-05-18 12:56:48PM -0700, Ricardo O. S. Soares wrote:
> Hi everybody,
> I'm working with a mixed membrane for the first time (POPC+POPE), and I want to restrain the all phosphors  (only Z axis). 
> However they belong to different [ moleculetype ] (ie. POPC and POPE), and GROMACS does not restrain more than one molecule type at a time.
> What implications would I have should I set both "POPC" and "POPE" to "Lipid", however in different itp files.
> Does anyone know a more elegant solution?
> Thanks
> Ricardo.
> ---
>  Ricardo O. S. Soares , PhD Student.
> Group of Biological Physics - Department of Physics & Chemistry
> Faculty of Pharmaceutical Sciences at Ribeirão Preto - University of São Paulo.
> Av.do Café, S/N - ZIP:14040-903 - Ribeirão Preto, São Paulo,  Brazil.
> Phone: +55 16 36024840. 
> Curriculum Lattes:http://lattes.cnpq.br/0777038258459931
> ross_usp at yahoo.com.br,rsoares at fcfrp.usp.br

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Peter C. Lai			| University of Alabama-Birmingham
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