Hi All,
I'm wondering if anyone has experienced what I'm seeing with Gromacs 4.5.5 on
GPU. It seems that certain systems fail inexplicably. The system I am working
with is a heterodimeric protein complex bound to DNA. After about 1 ns of
simulation time using mdrun-gpu, all the energies become NaN. The simulations
don't stop, they just carry on merrily producing nonsense. I would love to see
some action regarding http://redmine.gromacs.org/issues/941 for this reason ;)
I ran simulations of each of the components of the system individually - each
protein alone, and DNA - to try to track down what might be causing this
problem. The DNA simulation is perfectly stable out to 10 ns, but each protein
fails within 2 ns. Each protein has two domains with a flexible linker, and it
seems that as soon as the linker flexes a bit, the simulations go poof.
Well-behaved proteins like lysozyme and DHFR (from the benchmark set) seem fine,
but anything that twitches even a small amount fails. This is very unfortunate
for us, as we are hoping to see domain motions on a feasible time scale using
implicit solvent on GPU hardware.
Has anyone seen anything like this? Our Gromacs implementation is being run on
an x86_64 Linux system with Tesla S2050 GPU cards. The CUDA version is 3.1 and
Gromacs is linked against OpenMM-2.0. An .mdp file is appended below. I have
also tested finite values for cutoffs, but the results were worse (failures
occurred more quickly).
I have not been able to use the latest git version of Gromacs to test whether
anything has been fixed, but will post separately to gmx-developers regarding
the reasons for that soon.
-Justin
=== md.mdp ===
title = Implicit solvent test
; Run parameters
integrator = sd
dt = 0.002
nsteps = 5000000 ; 10000 ps (10 ns)
nstcomm = 1
comm_mode = angular ; non-periodic system
; Output parameters
nstxout = 0
nstvout = 0
nstfout = 0
nstxtcout = 1000 ; every 2 ps
nstlog = 5000 ; every 10 ps
nstenergy = 1000 ; every 2 ps
; Bond parameters
constraint_algorithm = lincs
constraints = all-bonds
continuation = no ; starting up
; required cutoffs for implicit
nstlist = 0
ns_type = grid
rlist = 0
rcoulomb = 0
rvdw = 0
; cutoffs required for qq and vdw
coulombtype = cut-off
vdwtype = cut-off
; temperature coupling
tc_grps = System
tau_t = 1.0 ; inverse friction coefficient for Langevin (ps^-1)
ref_t = 310
; Pressure coupling is off
Pcoupl = no
; Generate velocities is on
gen_vel = yes
gen_temp = 310
gen_seed = 173529
; Periodic boundary conditions are off for implicit
pbc = no
; Free energy must be off to use all-vs-all kernels
free_energy = no ; default, but just for the sake of being pedantic
; Implicit
implicit_solvent = GBSA
gb_algorithm = OBC
rgbradii = 0
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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