[gmx-users] confusion about implicint solvent
fracarb at myopera.com
Mon Sep 23 19:34:56 CEST 2013
Good afternoon everybody,
I'm a bit confuse about gromacs performances with implicit solvent.
I'm simulating a 1000 residues protein with explicit solvent, using both
a cpu and a gpu cluster.
With a gpu node (12 cores and 3 M2090 gpu ) I reach 10 ns/day, while
with no gpu and 144 cores I got 34 ns/day.
Because I have several mutants (more than 50) I have to reduce the
average simulation time and I was considering different option such as
the use of implicit solvent.
I tried with both the clusters and using gromacs 4.6 and 4.5 but the
performances are terrible (1 day for 100ps) comparing to the explicit
I read all the other messages on the mailing-list and the documentation,
but the mix of old and new "features"/posts really confuses me a lot.
it is said that with the gpu 4.5 and implicit solvent I should expect a
) I found this sentence "It is ultimately up to you as a user to decide
what simulations setups to use, but we would like to emphasize the
simply amazing implicit solvent performance provided by GPUs."
I follow the advise found in the mailing list and read both the
documentation (site and manual), but I can't figured it out what should
How can you guys have amazing performances?
I also found this answer from a last March post
that confuses me even more.
"Performance issues are known. There are plans to implement the implicit
solvent code for GPU and perhaps allow for better parallelization, but I
don't know what the status of all that is. As it stands (and as I have
said before on this list and to the developers privately), the implicit
code is largely unproductive because the performance is terrible. "
Should I skip the idea of using implicit solvent and try something else?
these are a set of parameters that I used (also the -pd flag)
; Run parameters
integrator = sd
tinit = 0
nsteps = 50000
dt = 0.002
; Output control
nstxout = 5000
nstvout = 5000
nstlog = 5000
nstenergy = 5000
nstxtcout = 5000
xtc_precision = 1000
energygrps = system
; Bond parameters
continuation = no
constraints = all-bonds
constraint_algorithm = lincs
lincs_iter = 1
lincs_order = 4
lincs_warnangle = 30
ns_type = simple
nstlist = 0
rlist = 0
rcoulomb = 0
rvdw = 0
coulombtype = cut-off
pbc = no
comm_mode = Angular
implicit_solvent = GBSA
gb_algorithm = OBC
nstgbradii = 1.0
rgbradii = 0
gb_epsilon_solvent = 80
gb_dielectric_offset = 0.009
sa_algorithm = Ace-approximation
sa_surface_tension = 0.0054
; Temperature coupling
tcoupl = v-rescale
tc_grps = System
tau_t = 0.1
ref_t = 310
; Velocity generation
gen_vel = yes
ld_seed = -1
thank you for the help.
Institute of Structural and Molecular Biology
fra.carbone.12 at ucl.ac.uk
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