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.
Thanks
em-vac-pbe.mdp
; 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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