Can't help you too much without more specific information. Post your
top and mdp files. Also post more information about when the error
occured (did any steps run before you get the crash?). set nstlog=1 in
your mdp so that you get the most information. That said, please try
these first before reposting:
- any errors or warning in grompp?
- did you remember to "define=-DFLEXIBLE" if you have waters
- turn off any pressure coupling
- try first with integrator=steep
- Here is a .mdp that I use for em, you could try it:
title = EnergyMinimization
cpp = /usr/bin/cpp
define = -DFLEXIBLE
integrator = steep
nsteps = 2000
tinit = 0
dt = 0.002
comm_mode = linear
nstcomm = 1
comm_grps = System
nstxout = 50000
nstvout = 50000
nstfout = 50000
nstlog = 1
nstlist = 10
nstenergy = 5000
nstxtcout = 5000
ns_type = grid
pbc = xyz
coulombtype = PME
rcoulomb = 0.9
fourierspacing = 0.12
pme_order = 4
vdwtype = cut-off
rvdw_switch = 0
rvdw = 1.4
rlist = 0.9
DispCorr = no
Pcoupl = no
tcoupl = no
annealing = no
gen_vel = yes
unconstrained-start = no
gen_temp = 300.
gen_seed = 9896
constraints = none
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