[gmx-users] about top and mdp

[nanyu101]

Hi,all gmx-users,
  There are some puzzles when I run grompp.
  I try to use make_hole program to make a hole in POPC.
  ./make_hole.pl -f popc128a.pdb -o popc.pdb -r 1.4 -lipat P8 -lipid POPC -cx 2.3 -cy 2.8 
  editconf -f popc.pdb -o popc.gro
  editconf -bt cubic -f popc.gro -o popc.gro -c -d 0.5
  genbox -cp popc.gro -cs spc216.gro -o popc_b4em.gro -p popc.top
  This is my popc.top after genbox.
#include "ffgmx_lipid.itp"
#include "popc.itp"
;#include "ions.itp"

#ifdef POSRES
#include "lipid_posre.itp"
#endif

#ifdef FLEX_SPC
#include "flexspc.itp"
#else
#include "spc.itp"
#endif


[ system ]
; name
popc + h2o

[ molecules ]
; name	number
POPC   106 

There is my em.mdp file.
cpp                 =  /lib/cpp
define              =  -DFLEX_SPC
constraints         =  none
integrator          =  steep
nsteps              =  100
;
;	Energy minimizing stuff
;
emtol               =  2000
emstep              =  0.01

nstcomm             =  1
ns_type             =  grid
rlist               =  1
rcoulomb            =  1.0
rvdw                =  1.0
Tcoupl              =  no
Pcoupl              =  no
gen_vel             =  no

grompp -f em.mdp -c popc_b4em.gro -p popc.top -o popc.tpr

After doing these, I just run grompp as tutorial in make_hole told.But when I run 
grompp -f run.mdp -s insert.tpr -c outbilayer.pdb -r outbilayer.pdb -p popc.top -o popc1.tpr, 
the system told me that -s is an unknown argument.At the same time,double outbilayer.pdb confused me too.

So  I try to run as below.
grompp -f run.mdp -c insert.tpr -r outbilayer.pdb -p popc.top -o popc1.tpr.

There are something confused me too.The top file is the same as shown above.But if I run run.mdp like below.
cpp                 =  /lib/cpp
define              =  -DPOSRES
constraints         =  none
integrator          =  steep
nsteps              =  100
;
;	Energy minimizing stuff
;
emtol               =  2000
emstep              =  0.01

nstcomm             =  1
ns_type             =  grid
rlist               =  1
rcoulomb            =  1.0
rvdw                =  1.0
Tcoupl              =  no
Pcoupl              =  no
gen_vel             =  no

The system told me that the coordinates in tpr file don't match the coordinates in popc.top( top coordinates is 0).I do not understant is. But if I run run.mdp like this:
cpp                 =  /lib/cpp
define              =  -DFLEX_SPC
constraints         =  none
integrator          =  steep
nsteps              =  100
;
;	Energy minimizing stuff
;
emtol               =  2000
emstep              =  0.01

nstcomm             =  1
ns_type             =  grid
rlist               =  1
rcoulomb            =  1.0
rvdw                =  1.0
Tcoupl              =  no
Pcoupl              =  no
gen_vel             =  no

The system give me results.

I am a novice in Gromacs.Any detailed information is recommended.
Thanks a lot.
Bests,
Xianhui

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