[gmx-users] Normal mode analysis problem

[jhon espinosa]

Hi all


I am running a normal mode analysis on a system with 1.05 million atoms without solvent.

I performed extensive double precision energy minimization using conjugate gradient (more than

14 days using 1024 processor). and my final values are:

Potential Energy  = -8.54191598792831e+06
Maximum force     =  2.40720622582240e+01 on atom 738910
Norm of force     =  3.52791700889658e-02

When I want to start the NMA I do:

aprun -n 1 grompp_mpi_d -f nma.mdp -c vault.EMCG.gro -p vault.top -o vault.nma1_d.tpr -t vault.EMCG.trr  -maxwarn -1

aprun -n 1024 mdrun_mpi_d -deffnm vault.nma1_d

And after a couple of hour I get and error :

Using compressed symmetric sparse Hessian format.
Allocating Hessian memory...

starting normal mode calculation 'GRoups of Organic Molecules in ACtion for Science in water'
2114424 steps.

Maximum force: 4.32366e+03
The force is probably not small enough to ensure that you are at a minimum.
Be aware that negative eigenvalues may occur
when the resulting matrix is diagonalized.

[NID 00116] 2016-09-19 04:25:18 Apid 6882392: initiated application termination
[NID 00116] 2016-09-19 04:25:20 Apid 6882392: OOM killer terminated this process.

Any suggestions ???

Thanks

Michael


the  nma.mdp is:

; RUN CONTROL PARAMETERS
integrator               = nm
t-init                   = 000
dt                       = 0.001
nsteps                   = 1

; OUTPUT CONTROL OPTIONS
nstxout                  = 1000
nstvout                  = 0
nstfout                  = 0
nstlog                   = 10000
nstenergy                = 10000
nstxtcout                = 50000

; NEIGHBORSEARCHING PARAMETERS
cutoff-scheme            = group
nstlist                  = 5
ns-type                  = Grid
pbc                      = xyz
rlist                    = 1.2

; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype              = Switch
rcoulomb                 = 1.0
rcoulomb_switch          = 0.8
epsilon_rf               = 1
vdw-type                 = Switch
rvdw                     = 1.0
rvdw_switch              = 0.8

; Temperature coupling
tcoupl                   = V-rescale
tc-grps                  = system
tau_t                    = 0.5
ref_t                    = 310