On 8/04/2010 4:23 PM, Evelyne Deplazes wrote:
Hi gmx-users
I am somehow famliar with gromacs but only used it with coarse grained
force fields (Martini) so far, not with all atom ones. I am now trying
to run a simulation on a membrane protein system (protein embedded in a
POPC bilayer solvated with water) using the gromos force field (Gromacs
4.0.2 ffG53a). Using gromacs tutorials I managed to create the required
input files (.gro, .top and .itp). I at at the stage of running a energy
minimization using position restraints on the protein and the peptide
molecules. I can grompp the input files
grompp -f min_posre.mdp -p topol.top -c system.gro -o topol.tpr -n index.ndx
with the following input file:
------------------------------
-------------------------------------------------------------------------------------
define = -DPOSRES -DPOSRES_LIPID
integrator = steep ; Algorithm (steep = steepest descent
minimization)
emtol = 100.0 ; Stop minimization when the maximum
force < 1000.0 kJ/mol/nm
emstep = 0.01 ; Energy step size
nsteps = 50000 ; Maximum number of (minimization) steps
to perform
; Parameters describing how to find the neighbors of each atom and how
to calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list
and long range forces
ns_type = grid ; Method to determine neighbor list
(simple, grid)
rlist = 1.2 ; Cut-off for making neighbor list
(short range forces)
coulombtype = PME ; Treatment of long range electrostatic
interactions
rcoulomb = 1.2 ; Short-range electrostatic cut-off
rvdw = 1.2 ; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions (yes/no)
-------------------------------------------------------------------------------------------------------------------
and the following topology file
-------------------------------------------------------------------------------------------------------------------
; Include forcefield parameters
#include "ffG53a6_lipid.itp"
; Include chain topologies
#include "protein.itp"
; Include Position restraint file
#ifdef POSRES
#include "posre_protein.itp"
#endif
; Include POPC topology
#include "popc.itp"
#ifdef POSRES_LIPID
#include "lipid_posre.itp"
#endif
; Include water topology
#include "spc.itp"
; Include generic topology for ions
#include "ions.itp"
[ system ]
; Name
mscl protein with POPC bilayer
[ molecules ]
; Compound #mols
Protein 1
POPC 242
SOL 32145
CL- 91
NA+ 91
-------------------------------------------------------------------------------------------------------------------
When I run the simulation I get the following output after 16 steps of
the minimisation
-------------------------------------------------------------------------------------------------------------------
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 100
Double precision normally gives you higher accuracy.
Steepest Descents converged to machine precision in 16 steps,
but did not reach the requested Fmax < 100.
Potential Energy = 8.0175742e+17
Maximum force = inf on atom 4443
Norm of force = inf
-------------------------------------------------------------------------------------------------------------------
It seems there is an infinite force on atom 4443 but I don't really
understand what that means. The confout.gro structure looks ok ie the
system has not "exploded". Should the protein not be restrained? How do
I know my position restraints actually work? I tried increasing the
force constant of the restraints or removing the restraints but still
get the same output. I also tried adding -DFLEXIBLE since I am using the
spc model, but still the same output.
can anyone tell me what that message actually means and what is wrong
with my system?
A useful diagnostic will be to remove the attempts to use position
restraints in the "define = " line. If you still get an error like this,
then your problem (massive positive energy, infinite forces) is almost
certainly a severe atomic overlap, possibly near atom 4443. If so, get
out a visualization program and look for water overlapping lipid, or
something. Position restraints won't help resolve gross errors like that...
Mark
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