[gmx-users] speed issue, gmx runtime estimate = f(t)

[Michael Brunsteiner]

Dear all, 

I am trying to optimize runtimes/speed for a series of
calculations i plan to do with a rather complex system.
When looking at runtimes I observed one peculiar issue:
the estimated runtime written to stderr by mdrun with the "-v"
option keepsgrowing ... in my experience this estimate normally
converges to a fairly accurate value within a few hundred
steps. not so here ..
for example, starting a job at 12:14 gromacs writes to stderr:

step 100, will finish Wed Apr  6 12:40:35 2011vol 0.97  imb F  1% 
step 200, will finish Wed Apr  6 12:39:42 2011vol 0.95  imb F  2%
step 300, will finish Wed Apr  6 12:39:47 2011vol 0.95  imb F  1%
step 400, will finish Wed Apr  6 12:39:52 2011vol 0.96  imb F  1%
...
step 38400, will finish Wed Apr  6 14:09:11 2011vol 0.91  imb F 29% 

so the estimated run time grows steadily from 25 to 110 minutes 
within about one hour...
this is mdrun_d (gmx-4.5.3) running on a linux PC with 
2 processores/4 nodes/8 threads. There's a couple of other programs (X, editor, 
...)
running at the same time but none of them uses a lot of CPU.

Anyway, what i see lets me expect there might be a way 
to speed up these calculations. I'd appreciate any suggestions!
(below is my mdp file.)

cheers,
Michael


mdp file:

integrator           = md
;
dt                   = 0.001
tinit                = 0
nsteps               = 100000
nstxtcout            = 0
nstxout              = 1000
nstvout              = 0
nstfout              = 0
nstenergy            = 1000
;
constraint_algorithm = lincs
constraints          = hbonds
;
comm_mode            = Linear
nstcomm              = 1
pbc                  = xyz
nstlist              = 10
ns_type              = grid 
rlist                = 1.4
rcoulomb             = 1.4
rvdw                 = 1.4
;
coulombtype          = PME
vdwtype              = User
fourierspacing       = 0.2
optimize_fft         = yes
;
Tcoupl               = nose-hoover
tc_grps              = System
ref_t                = 300.0
tau_t                = 0.4
gen_vel              = yes
gen_temp             = 240.0
gen_seed             = 222222
;
pull                 = umbrella
pull_geometry        = distance
pull_dim             = N N Y
pull_start           = yes
pull_ngroups         = 1
pull_group0          = f1
pull_group1          = f2
pull_rate1           = -0.015
pull_k1              = 1000
pull_nstxout         = 100
pull_nstfout         = 100
pull_pbcatom0        = 241
pull_pbcatom1        = 482
;
freezegrps           = c1 c2
freezedim            = Y Y N Y Y N
;
energygrps           = SOL CC CF
energygrp_table      = CF CF  CF SOL  CF CC