[gmx-users] Differences between 4.5.5 and 4.6.2-dev?

[Stefan Kesselheim]

Dear Gromacs users,
a short disclaimer first: I'm new to using GROMACS and new to doing atomistic resolution modelling. If I'm doing anything very wrong, I'd be very happy to hear. 

I'm trying to simulate ion current in a nanopore. My nanopore consists of LJ particles positioned on the surface of a cylinder, that is closed with itself over PBC, thus my system is quasi-infinite. The pore is filled with SPC/E water and (in this particular simulation) 128 NA+ and CL- ions where I'm using the gromos53a6 ion parameters. An electric field is applied in the periodic direction. The current is then the sum of the distances traveled by all ions in a production run divided by the length of the box times +- 1 (depending on the ion species), divided by the simulation time. 

I noticed now the following: 
With GROMACS 4.5.5 and 4.6.2 I obtained different values for the currents; the NA ions travel faster in 4.6.2 while the Cl ions travel faster in 4.5.5. The difference is about 20% in both cases and it is statistically significant (5 or more sigma). 

I'm using PME for electrostatics as later a DNA molecule will be added, and the long range nature of electrostatics will most likely be quite important. I am using a twin range cutoff scheme with 
rlist                    = 0.9
rcoulomb                 = 0.9
rvdw                     = 1.4
and
ewald_rtol               = 1e-05
and the default fourier_spacing (which should be 1.2 nm).
According to g_pme_error this choice is not particularly smart (I will do better, I promise) but however should not explain any differences between the two versions.

Comparing the gmxdump output of both tprs i noticed the following differences:
4.6.2          						|  		4.5.5
  verlet-buffer-drift  = 0.005                    |          verlet-buffer-drift  = 0    
  fourierspacing       = 0.12                     |          fourierspacing       = 0    
   dihre-fc             = 0                        |        dihre-fc             = 1000      

These parameters are my top candidates to explain differences, but I have attached the rest of the production run mdp below.

My 4.5.5 version was the official one compiled on our local supercomputer (by the admins) and my 4.6.2 version is from the git repository, branch release-4.6, last commit 873b98540a47a5727e69342117ab71f8c8b75072. No GPU usage involved. 4.5.5 with "usual" mpi, 4.6.2 with thread-mpi. 

Can anybody think of an explanation? My hope would be that some default behaviour has changed between the versions. 
My short-term strategy is rerunning with a single cutoff of 1.4, an optimal choice of ewald_rtol (tuned with g_pme_error) and hope that the differences disappear. This however will take a while.
Cheers and thanks in advance
Stefan Kesselheim


Here is the rest of my mdp file.

define                   = -DPOSRES_P
integrator               = md
tinit                    = 0
dt                       = 0.002
nsteps                   = 4000000
init_step                = 0
comm_mode                = None
nstxout                  = 0
nstvout                  = 0
nstfout                  = 0
nstxtcout		 = 100
nstcheckpoint            = 10000
nstlog                   = 10000
nstenergy                = 1000
energygrps               = POR SOL NA CL
energygrp_excl           = POR POR
nstlist                  = 5
ns_type                  = grid
pbc                      = xyz
periodic_molecules       = yes
rlist                    = 0.9
domain-decomposition     = yes
coulombtype              = PME
rcoulomb-switch          = 0
rcoulomb                 = 0.9
epsilon_r                = 1
epsilon_rf               = 1
vdwtype                  = Cut-Off
rvdw-switch              = 0.
rvdw                     = 1.4
DispCorr                 = EnerPres
table-extension          = 1
energygrp_table          = 
fourier_nx               = 0
fourier_ny               = 0
fourier_nz               = 0
; EWALD/PME/PPPM parameters
pme_order                = 4
ewald_rtol               = 1e-05
ewald_geometry           = 3d
epsilon_surface          = 0
optimize_fft             = no
implicit_solvent         = No
tcoupl                   = v-rescale 
tc-grps                  = Water_and_ions POR 
tau-t                    = 5.0 5.0  
ref-t                    = 300 300 
nsttcouple               = 1
pcoupl			 = no 
Pcoupltype               = Isotropic
tau-p                    = 1.0
compressibility          = 4.5e-5
ref-p                    = 1.0
gen_vel                  = yes
gen_temp                 = 300
gen_seed                 = 32293
ld_seed                 = 32293
E-x                      = 
E-xt                     = 
E-y                      = 
E-yt                     = 
E-z                      = 1 0.2 0 
E-zt                     = 
constraints              = hbonds


-----------------------------------------------
Stefan Kesselheim
Institute for Computational Physics
Allmandring 3
+49 711 685 63630
70184 Stuttgart
kessel at icp.uni-stuttgart.de