Hi,

I am trying to prepare a simple system for tests with CUDA. My guinea pig is the lysozyme system from this tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/01_pdb2gmx.html

but I prepared it using the AMBER99sb-ildn force field and the SPCE water model.

After extensive minimization steps, I started a (CPU) very short test run (3 ns) to check if everything was ok before beginning to deal with CUDA.

However I found that there is a strong drift in energy and temperature:

>>>>>g_energy_d output:

 Opened 1AKI_production_GPU.edr as double precision energy file

 Select the terms you want from the following list by
 selecting either (part of) the name or the number or a combination.
 End your selection with an empty line or a zero.
 -------------------------------------------------------------------
1 Bond 2 Angle 3 Proper-Dih. 4 Improper-Dih. 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total- Energy 13 Temperature 14 Pressure 15 Box-X 16 Box-Y 17 Box-Z 18 Volume 19 Density 20 pV 21 Enthalpy 22 Vir-XX 23 Vir-XY 24 Vir-XZ 25 Vir-YX 26 Vir-YY 27 Vir-YZ 28 Vir-ZX 29 Vir-ZY 30 Vir-ZZ 31 Pres-XX 32 Pres-XY 33 Pres-XZ 34 Pres-YX 35 Pres-YY 36 Pres-YZ 37 Pres-ZX 38 Pres-ZY 39 Pres-ZZ 40 #Surf*SurfTen 41 Box-Vel-XX 42 Box-Vel-YY 43 Box-Vel-ZZ 44 Mu-X 45 Mu-Y 46 Mu-Z 47 Coul-SR:Protein-Protein 48 LJ-SR:Protein-Protein 49 Coul-14:Protein-Protein 50 LJ-14:Protein-Protein 51 Coul-SR:Protein-non-Protein 52 LJ-SR:Protein-non-Protein 53 Coul-14:Protein-non-Protein 54 LJ-14:Protein-non-Protein 55 Coul-SR:non-Protein-non-Protein 56 LJ-SR:non-Protein-non-Protein 57 Coul-14:non-Protein-non-Protein 58 LJ-14:non-Protein-non-Protein
  59  T-System

10
11
12
13
14

 Last energy frame read 30000 time 5000.000

Statistics over 3000001 steps [ 2000.0000 through 5000.0000 ps ], 5 data sets
 All statistics are over 1500001 points

 Energy                      Average   Err.Est.       RMSD  Tot-Drift

-------------------------------------------------------------------------------
Potential -529618 1500 3004.68 -10322.5 (kJ/mol) Kinetic En. 86141.8 610 1295.7 -4294.67 (kJ/mol) Total Energy -443476 2100 4220.26 -14617.1 (kJ/mol)
 Temperature                  292.49        2.1    4.39949   -14.5823   (K)
Pressure 1.02119 0.0046 133.601 -0.0134421 (bar)

 You may want to use the -driftcorr flag in order to correct
 for spurious drift in the graphs. Note that this is not
 a substitute for proper equilibration and sampling!

 WARNING: nmol = 1, this may not be what you want.

Temperature dependent fluctuation properties at T = 292.49.


The MDP is:

>>>>>production_GPU.mdp

; PREPROCESSING OPTIONS
title                   = production run 1 for GPU usage
include                 =
define                  =
; RUN CONTROL PARAMETERS
integrator = md ; for GPUs: "Option md is accepted but keep in mind that the actual algorithm is not leap-frog."

tinit                   = 2000
dt                      = 0.001         ; 1 fs
nsteps                  = 3000000       ; 3 ns
init_step               = 0
; CENTER OF MASS MOTION REMOVAL
nstcomm                 = 1
comm_mode               = linear
comm_grps               = protein non-protein
; OUTPUT CONTROL
nstxout = 2000 ; Doubled these because disk output is a strong bottleneck apparently

nstvout                 = 2000
nstfout                 = 0
nstlog                  = 100
nstenergy               = 100
nstxtcout               = 100
nstcalcenergy           = -1
xtcprecision            = 1000
energygrps              = protein non-protein
; NEIGHBOR SEARCHING PARAMETERS
nstlist                 = 2.
ns_type                 = grid
pbc                     = xyz
rlist                   = 1.0
; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype             = PME           ; this is OK for GPUs
rcoulomb_switch         = 0.
rcoulomb                = 1.0
epsilon_r               = 1
vdwtype                 = cut-off
rvdw-switch             = 0.
rvdw                    = 1.0
DispCorr                = no
fourierspacing          = 0.12
fourier_nx              = 0
fourier_ny              = 0
fourier_nz              = 0
pme_order               = 4
ewald_rtol              = 1e-05
epsilon_surface         = 0
optimize_fft            = no
; TEMPERATURE COUPLING
tcoupl = andersen ; All values of this are equivalent to "andersen" in GPU mode
tc_grps                 = system
tau_t                   = 0.1
ref_t                   = 300.00
; PRESSURE COUPLING
pcoupl = parrinello-rahman ; "OpenMM implements the Monte Carlo barostat. All values for Pcoupl are thus accepted."

pcoupltype              = isotropic
tau_p                   = 1.0
compressibility         = 4.5e-05
ref_p                   = 1.0
; VELOCITY GENERATION
gen_vel                 = no

<<<<<<<<

Command lines are:

grompp_d -f production_GPU.mdp -c 1AKI_em4sol.gro -p topol.top -o 1AKI_production_GPU.tpr

mpirun -np 8 mdrun_d -v -deffn 1AKI_production_GPU -s 1AKI_production_GPU.tpr -g 1AKI_production_GPU.log -c 1AKI_production_GPU.gro -o 1AKI_production_GPU.trr -g 1AKI_production_GPU.log -e 1AKI_production_GPU.edr

I am using Gromacs 4.5.5 compiled in double precision.

I am very rusty with Gromacs, since I last dealt molecular dynamics more than 1 year ago :) , so probably I am missing something obvious. Any hint on where should I look for to solve the problem? (Also, advice on if the .mdp is indeed correct for CUDA simulations are welcome)

cheers,
Massimo



--
Massimo Sandal, Ph.D.
http://devicerandom.org
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