[gmx-users] xx of the xxxx bonded interactions couldn't be calculated

[Badamkhatan]

Dear GMX-users

Recently i got this error and note from my MD2 simulation. I'm solvating
1-octanol to 1-octanol and calculating free energy differences. This is the
last step of my calculation and previous steps are looking fine. Basically i
followed Justin's free energy tutorial. 
Here is 
Note:
 A list of missing interactions:
LJC Pairs NB of210 missing  1
  exclusions of  25308 missing  1

Molecule type '1-octanol'
the first 10 missing interactions, except for exclusions:
LJC Pairs NB atoms3   25   global 325

Fatal error: 
2 of the 57736 bonded interactions could not be calculated because some
atoms involved moved further apart than the multi-body cut-off distance (1
nm) or the two-body cut-off distance (1 nm), see option -rdd, for pairs and
tabulated bonds also see option -ddcheck

Please help me and suggest any idea to solve this problem?





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[gmx-users] Error of violate the Second Law of Thermodynamics in Free energy calculation with BAR

[badamkhatan togoldor]

Dear GMX users

Hi. I'm calculating some small organic molecule's desolvation free energy. 
Recently i got this error from BAR calculation. Please anyone explain what's 
wrong in here?  

First:
WARNING: Using the derivative data (dH/dlambda) to extrapolate delta H values.
This will only work if the Hamiltonian is linear in lambda.

and then Second:
WARNING: Some of these results violate the Second Law of Thermodynamics: 
 This is can be the result of severe undersampling, or (more likely)
 there is something wrong with the simulations.

I have two MD simulation steps. For example desolvation free energy of 
chloroform and methanol:
The final result from MD1 something like this:
total   0.000 -  1.000,   DG  7.72 +/-  0.05

The final result from MD2 something like this:
total   0.000 -  1.000,   DG  3.96 +/-  0.06

Total Gibbs energy of desolvation 11.7 +/- 0.1 kJ/mol  (including with these 
two warnings)

Something wrong in MD?  
MD1.mdp
;Run control
integrator   = sd   ; Langevin dynamics
tinit    = 0
dt   = 0.002
nsteps   = 100  ; 2 ns
nstcomm  = 100
; Output control
nstxout  = 500
nstvout  = 500
nstfout  = 0
nstlog   = 500
nstenergy    = 500
nstxtcout    = 0
xtc-precision    = 1000
; Neighborsearching and short-range nonbonded interactions
nstlist  = 10
ns_type  = grid
pbc  = xyz
rlist    = 1.0
; Electrostatics
coulombtype  = PME
rcoulomb = 1.0
; van der Waals
vdw-type = switch
rvdw-switch  = 0.8
rvdw = 0.9
; Apply long range dispersion corrections for Energy and Pressure
DispCorr  = EnerPres
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12
; EWALD/PME/PPPM parameters
pme_order    = 6
ewald_rtol   = 1e-06
epsilon_surface  = 0
optimize_fft = no
; Temperature coupling
; tcoupl is implicitly handled by the sd integrator
tc_grps  = system
tau_t    = 0.2
ref_t    = 300
; Pressure coupling is on for NPT
Pcoupl   = Parrinello-Rahman 
tau_p    = 5
compressibility  = 4.5e-05
ref_p    = 1.0 
; Free energy control stuff
free_energy  = yes
init_lambda  = 0.0
delta_lambda = 0
foreign_lambda   = 0.05
sc-alpha = 0.5
sc-power = 1.0
sc-sigma = 0.3 
couple-lambda0   = vdw-q  ; only van der Waals interactions
couple-lambda1   = vdw ; turn off everything, in this case only vdW
couple-intramol  = no
nstdhdl  = 10
; Do not generate velocities
gen_vel  = no 
; options for bonds
constraints  = all-bonds  ; 
; Type of constraint algorithm
constraint-algorithm = lincs
; Constrain the starting configuration
; since we are continuing from NPT
continuation = yes 
; Highest order in the expansion of the constraint coupling matrix
lincs-order  = 12

MD2.mdp
;Run control
integrator   = sd   ; Langevin dynamics
tinit    = 0
dt   = 0.002
nsteps   = 100  ; 2 ns
nstcomm  = 100
; Output control
nstxout  = 500
nstvout  = 500
nstfout  = 0
nstlog   = 500
nstenergy    = 500
nstxtcout    = 0
xtc-precision    = 1000
; Neighborsearching and short-range nonbonded interactions
nstlist  = 10
ns_type  = grid
pbc  = xyz
rlist    = 1.0
; Electrostatics
coulombtype  = PME
rcoulomb = 1.0
; van der Waals
vdw-type = switch
rvdw-switch  = 0.8
rvdw = 0.9
; Apply long range dispersion corrections for Energy and Pressure
DispCorr  = EnerPres
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12
; EWALD/PME/PPPM parameters
pme_order    = 6
ewald_rtol   = 1e-06
epsilon_surface  = 0
optimize_fft = no
; Temperature coupling
; tcoupl is implicitly handled by the sd integrator
tc_grps  = system
tau_t    = 0.2
ref_t    = 300
; Pressure coupling is on for NPT
Pcoupl   = Parrinello-Rahman 
tau_p    = 5
compressibility  = 4.5e-05
ref_p    = 1.0 
; Free energy control stuff
free_energy  = yes
init_lambda  = 0.0
delta_lambda = 0
foreign_lambda   = 0.05
sc-alpha = 0.5
sc-power = 1.0
sc-sigma