Hi gmx-users<br><br>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 <br>
<br>grompp -f min_posre.mdp -p topol.top -c system.gro -o topol.tpr -n index.ndx<br><br>with the following input file:<br><br>------------------------------<div id=":yc" class="ii gt">-------------------------------------------------------------------------------------<br>
define = -DPOSRES -DPOSRES_LIPID<br>integrator = steep ; Algorithm (steep = steepest descent minimization)<br>emtol = 100.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm<br>
emstep = 0.01 ; Energy step size<br>nsteps = 50000 ; Maximum number of (minimization) steps to perform<br><br>; Parameters describing how to find the neighbors of each atom and how to calculate the interactions<br>
nstlist = 1 ; Frequency to update the neighbor list and long range forces<br>ns_type = grid ; Method to determine neighbor list (simple, grid)<br>rlist = 1.2 ; Cut-off for making neighbor list (short range forces)<br>
coulombtype = PME ; Treatment of long range electrostatic interactions<br>rcoulomb = 1.2 ; Short-range electrostatic cut-off<br>rvdw = 1.2 ; Short-range Van der Waals cut-off<br>
pbc = xyz ; Periodic Boundary Conditions (yes/no)<br>-------------------------------------------------------------------------------------------------------------------<br><br>and the following topology file<br>
<br>-------------------------------------------------------------------------------------------------------------------<br>; Include forcefield parameters<br>#include "ffG53a6_lipid.itp"<br><br>; Include chain topologies<br>
#include "protein.itp"<br><br>; Include Position restraint file<br>#ifdef POSRES<br>#include "posre_protein.itp"<br>#endif<br><br>; Include POPC topology<br>#include "popc.itp"<br><br>#ifdef POSRES_LIPID<br>
#include "lipid_posre.itp"<br>#endif<br><br>; Include water topology<br>#include "spc.itp"<br><br>; Include generic topology for ions<br>#include "ions.itp"<br><br>[ system ]<br>; Name<br>mscl protein with POPC bilayer<br>
<br>[ molecules ]<br>; Compound #mols<br>Protein 1<br>POPC 242<br>SOL 32145<br>CL- 91<br>NA+ 91<br>-------------------------------------------------------------------------------------------------------------------<br>
<br>When I run the simulation I get the following output after 16 steps of the minimisation<br>-------------------------------------------------------------------------------------------------------------------<br>Stepsize too small, or no change in energy.<br>
Converged to machine precision,<br>but not to the requested precision Fmax < 100<br><br>Double precision normally gives you higher accuracy.<br><br>Steepest Descents converged to machine precision in 16 steps,<br>but did not reach the requested Fmax < 100.<br>
Potential Energy = 8.0175742e+17<br>Maximum force = inf on atom 4443<br>Norm of force = inf<br>-------------------------------------------------------------------------------------------------------------------<br>
<br>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. <br>
<br>can anyone tell me what that message actually means and what is wrong with my system?<br><br>thanks </div><br clear="all"><br>-- <br>Evelyne Deplazes<br><br>PhD student <br>Theoretical Chemistry group<br>University of Western Australia <br>
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