[gmx-users] Strange energy values with GMX 5.1, PME and Verlet

[Diana Lousa]

Dear all,

For testing purposes, I performed a short simulation (10 ps) of a CL- and a
Na+ ion in vacuum with gmx 5.1.4 and compared the Group and Verlet cutoff
schemes. I ran gmx energy to monitor the interaction energy between the
ions and obtained the following results:

1) Verlet
Energy                      Average   Err.Est.       RMSD  Tot-Drift
-------------------------------------------------------------------------------
Pressure                   0.128465      0.044    15.8209   -0.27251  (bar)
Coul-SR:NA-NA              -244.832          0       -nan -4.68375e-14
(kJ/mol)
LJ-SR:NA-NA                       0          0          0          0
(kJ/mol)
Coul-SR:NA-CL              -153.193        7.4    32.7214   -43.0706
(kJ/mol)
LJ-SR:NA-CL                 42.5252        1.7    20.9531    9.65428
(kJ/mol)
Coul-SR:CL-CL              -244.832          0       -nan -4.68375e-14
(kJ/mol)
LJ-SR:CL-CL                       0          0          0          0
(kJ/mol)

2) Group
Energy                      Average   Err.Est.       RMSD  Tot-Drift
-------------------------------------------------------------------------------
Pressure                  0.0159313      0.039    17.1949   0.303503  (bar)
Coul-SR:NA-NA                     0          0          0          0
(kJ/mol)
LJ-SR:NA-NA                       0          0          0          0
(kJ/mol)
Coul-SR:NA-CL              -152.361          8    33.2265   -46.2306
(kJ/mol)
LJ-SR:NA-CL                 42.2222        1.9    22.5877    11.0263
(kJ/mol)
Coul-SR:CL-CL                     0          0          0          0
(kJ/mol)
LJ-SR:CL-CL                       0          0          0          0
(kJ/mol)

As you can see, the Coul-SR:NA-NA and Coul-SR:CL-CL have the value of
-244.832 when using Verlet, which is very strange. This does not happen
when using Group cutoff or when using Verlet in GMX 4.5 (the value is 0 in
these cases).
GMX 2016 gives similar results to GMX 5.1.4:

3) Verlet GMX 2016:
Energy                      Average   Err.Est.       RMSD  Tot-Drift
-------------------------------------------------------------------------------
Pressure                 -0.0106255       0.22    19.2119   0.756146  (bar)
Coul-SR:NA-NA              -244.832          0       -nan -4.68375e-14
(kJ/mol)
LJ-SR:NA-NA                       0          0          0          0
(kJ/mol)
Coul-SR:NA-CL              -150.921        7.9     35.159   -45.7216
(kJ/mol)
LJ-SR:NA-CL                 42.0629          2    25.1668    11.2282
(kJ/mol)
Coul-SR:CL-CL              -244.832          0       -nan -4.68375e-14
(kJ/mol)
LJ-SR:CL-CL                       0          0          0          0
(kJ/mol)

I am not using GPUs, since I know you cannot monitor energy groups when
using GPUs.
Does anyone have any idea why this happens and what consequences does it
have?


Here's the mdp:

****************************
define              =
integrator          =  md
tinit               =  0.0
dt                  =  0.002
nsteps              =  5000
nstcomm             =  1
nstxtcout           =  500
xtc-precision       =  1000
nstxout             =  0
nstvout             =  0
nstfout             =  0
nstlog              =  10
nstenergy           =  1

nstlist             =  20
ns_type             =  grid

;PME
rlist               = 1.0
coulombtype         = PME
rcoulomb            = 1.0
fourierspacing      = 0.16
pme_order           = 4
vdwtype             = cut-off
rvdw                = 1.0
cutoff-scheme         = Verlet ; or Group

; Energy monitoring
energygrps          =  NA CL

Tcoupl              =  v-rescale
tc-grps             =  Ion
tau_t               =  0.10
ref_t               =  300.0

; Isotropic pressure coupling is now of
; Pcoupl              =  berendsen
Pcoupl              =  No


; lincs_
constraint_algorithm=lincs
lincs_order         =  8
constraints         = none
lincs-warnangle     =  90


​Thanks in advance
Best regards​

-- 
Diana Lousa
Post-doc
Protein Modeling Laboratory
ITQB/UNL
Oeiras, Portugal