[gmx-users] Help with energygrp_excl

toma0052 toma0052 at umn.edu
Thu Feb 8 04:12:12 CET 2007

     I am doing some simulations on a DPPC bilayer that I got from Dr.
Tieleman's website.  I would like to examine shear forces necessary for
membrane rupture.  To do this, I have applied an acceleration to the head
(First 12 atoms of each DPPC molecule, as numbered in the topology file) of
the upper leaflet while keeping the positions of the same 12 atoms of the
bottom leaflet restrained.  The rest of the atoms of the DPPC molecules are
free to go where the forces take them.
     After the md run, the numbers that I get for the pressure and the
surface tension of the system are much larger than I would expect them to be.
 I am assuming that this is because of the restrained atoms, so I would like
to add to my .mdp file energy group exclusions.  However, if I define my
energy groups as:

energygrp          = DPPC SOL acc res
energygrp_excl     = res res  res DPPC  res SOL  res acc

I get the error that some atoms belong to more than one energy group when
putting everything through grompp.
     So, when I make another group that is all atoms not res (the restrained
atoms, I called energy1) and do:

energygrp          = res energy1
energygrp_excl     = res res  res energy1

I get a different error that says "atoms 3212 and 3213 in charge group 2179
are in different energy groups".  However, this seems to be what I want,
since atom 3213 is in the group that is restrained whereas atom 3212 is not.
     Am I setting up energy group exclusions incorrectly?  How do I exclude
the contributions from the restrained atoms in my pressure and surface
tension calculations?

Thank you,
Mike Tomasini

Here is my mdp file if that in any way helps:

title			 = DPPC shear simulation
cpp			 = /lib/cpp
:Directories to include in the topology format
include			 = -I.../top
;Include definition for position restraints
define			 = -DPOSRES
integrator		 = md
;Simulation time of 100 ps
dt			 = 0.002    ; In picoseconds
nsteps		 	 = 50000
nstxout			 = 100
nstvout 		 = 100
nstfout			 = 1000 
nstlog  		 = 10
nstenergy		 = 10
nstlist			 = 5
ns_type			 = grid
rlist			 = 0.9
coulombtype		 = PME
rcoulomb		 = 0.9
rvdw			 = 1.4
fourierspacing		 = 0.12
fourier_nx		 = 0
fourier_ny		 = 0
fourier_nz		 = 0
pme_order		 = 4
ewald_rtol		 = 1e-5
optimize_fft		 = yes
pbc			 = xyz
;Temperature Coupling
tcoupl  		 = berendsen
tc-grps 		 = DPPC SOL   
tau_t			 = 0.1 0.1  
ref_t			 = 310 310
;Pressure Coupling
Pcoupl  		 = berendsen
Pcoupltype               = isotropic
tau_p			 = 0.5
compressibility 	 = 4.5e-5
ref_p			 = 1.0
;Velocity generation
gen_vel 		 = yes 
gen_temp		 = 310
gen_seed		 = 133529
;Energy group exclusion for position restraints
energygrps		 = res energy1
energygrp_excl		 = res res  res energy1  ;Correct?
;energygrps		 = res acc DPPC SOL
;energygrp_excl		 = res res  res acc  res DPPC  res SOL
;Accelerate top layer
acc_grps		 = acc
accelerate		 = 1.0 0.0 0.0
;Freeze bottom layer
freezegrps		 = res
freezedim		 = Y Y Y

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