[gmx-users] Restarting minimization

Juan Antonio Raygoza Garay raygozag at psu.edu
Sat Apr 6 20:23:59 CEST 2013

Hi, i'm new to grimaces and want to run a minimization process in parts, but i'm having problems extracting the last frame, when i try the following command:

trjconv -s em-vac${ID}.tpr -f em-vac${ID}.trr -o mintmp.pdb -e 0

it returns no data, if i try 11 in the frame number it prints out  a model, but when trying to run mintmp.pdb, i get the following error:

Fatal error:
There is no domain decomposition for 8 nodes that is compatible with the given box and a minimum cell size of 23.38 nm
Change the number of nodes or mdrun option -rdd
Look in the log file for details on the domain decomposition

what am i doing wrong? or is there a tutorial where someone does this.



; Define can be used to control processes
define = -DFLEXIBLE ; Use flexible water model
; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 500.0 ; Stop minimization when the maximum force < 1.0 kJ/mol
nsteps = 100 ; Maximum number of (minimization) steps to perform
nstenergy = 1 ; Write energies to disk every nstenergy steps
energygrps = System ; Which energy group(s) to write to disk
nstlist = 1 ; Frequency to update the neighbor list
ns_type = grid ; Method to determine neighbor list (simple, grid)
coulombtype = PME ; Treatment of long range electrostatic interactions
rlist = 1.0 ; Cut-off for making neighbor list (short range forces)
rcoulomb = 1.0 ; long range electrostatic cut-off
rvdw = 1.0 ; long range Van der Waals cut-off
constraints = none ; Bond types to replace by constraints
pbc = xyz ; Periodic Boundary Conditions

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