[gmx-users] creating a "solid" layer

Oliver Beckstein oliver at biop.ox.ac.uk
Tue Feb 10 00:47:01 CET 2004

Hi Shuaib,

I attached a script that I use to make dummy layers (made from unified CH4 
molecules) and the corresponding itp files that you can include in your 
topology. Basically, it's doing what David suggested. After changing the 
path at the top to your gmx installation you run

   mkslab.sh 4 5 0.4 slab.pdb

to create a pdb (or gro, if you want) file with X=4nm, Y=5nm and thickness 
0.4nm. Because the CH4 have a diameter of 0.39nm this should give you one 
layer. Then center and solvate using genbox. Your topology would look 
something like

; topology for membrane mimetic
#include "ffgmx.itp"
#include "mth.itp"
#include "lay.itp"
#include "spc.itp"
[ system ]
; name
Hydrophobic dummy membrane, solvated in water
[ molecules ]
LAY   675
SOL   3910

Of course, you have to check that the numbers for LAY and SOL correspond 
to your input file.

Note that I hid the restraints for the LAY atoms in lay.itp.

Btw, I'd suggest at least 1.5nm of water on either side; check that your
diffusion coefficient approaches its bulk value (from a separate
simulation of a pure box of water) far from the slab in its components 
parallel and perpendicular to the membrane. If you are going to look at 
ions be prepared to wait for a while for equilibration---20ns and more.


Oliver Beckstein * oliver at biop.ox.ac.uk

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[ moleculetype ]
;name  nrexcl
  LAY       3

[ atoms ]
;   nr     type    resnr    res atom     cgnr charge         mass
     1      CH4        1    LAY CH4         1  0.000         16.04300

#ifdef POSRE
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
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;;; only ONE defaults entry !!!
;;; 2002-05-06
;[ defaults ]
; nbfunc	comb-rule	gen-pairs	fudgeLJ	fudgeQQ
;  1		1		no		1.0	1.0

#ifdef _FF_GROMACS
[ atomtypes ]
;name        mass      charge   ptype            c6           c12
  CH4    16.0430       0.000       A   0.01317904  3.4363044e-05

[ bondtypes ]
;ai      aj   func        b0[nm]    kB[kJ mol^-1 nm^-2]
CH4     CH4      1         0.400    5.0e+05

; Gromos96 has got CH4 but not the mass ??
#ifdef _FF_GROMOS96
[ atomtypes ]
CH4     16.0430      0.000     A  0.01317904  3.4363044e-05

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