[gmx-users] 1-4 interactions free energy calculations

Sonia Aguilera sm.aguilera37 at uniandes.edu.co
Mon Jun 24 19:07:34 CEST 2013

Hi all!

I have been running a series of simulations for coupling a molecule (free
energy calculations). All my settings and parameters in the mdp file worked
great for one system, but then I change the molecule to a bigger one and I
started to have warnings about 1-4 interactions:

Warning: 1-4 interaction between 1 and 143 at distance 2.579 which is larger
than the 1-4 table size 2.500 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size

I made severals tests to find the error: minimization, nvt, mdp and md
without the Free Energy settings and It ran without the warning. So I guess
the warning must be related to the FE implementation. However, I'm clueless
about what can I change to stop having that warning. I already read other
posts but I'm still the same. Should I just ignore it? Also, the initial
structure is the result of a md simulation, so I don't know what can be
wrong in the topology or mdp file.  Should I change the continuation
parameter (continuation=yes) for the minimization and the nvt? 

Energy minimization converged but not to machine precision:

Converged to machine precision,
but not to the requested precision Fmax < 100

Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 481 steps,
but did not reach the requested Fmax < 100.
Potential Energy  = -7.8070088e+05
Maximum force     =  7.6036969e+02 on atom 68
Norm of force     =  2.3164215e+01

This is the copy of the mdp file (based os Justin Lemluk's tutorial), I'm
using GROMACS 4.5.4.

title                    = steepest descent energy minimization
; Run control
integrator               = steep
nsteps                   = 30000
; EM criteria and other stuff
emtol                    = 100
emstep                   = 0.01
niter                    = 20
nbfgscorr                = 10
; Output control
nstlog                   = 1
nstenergy                = 1
; Neighborsearching and short-range nonbonded interactions
nstlist                  = 1
ns_type                  = grid
pbc                      = xyz
periodic-molecules       = yes
rlist                    = 1.5
; Electrostatics
coulombtype              = PME
rcoulomb                 = 1.5
; 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 PMEPPPM FFT grid
fourierspacing           = 0.12
; EWALDPMEPPPM parameters
pme_order                = 6
ewald_rtol               = 1e-06
epsilon_surface          = 0
optimize_fft             = no
; Temperature and pressure coupling are off during EM
tcoupl                   = no
pcoupl                   = no
; Free energy control stuff
free_energy              = yes
init_lambda              = 1.0
delta_lambda             = 0
foreign_lambda           = 0.95
sc-alpha                 = 0
sc-power                 = 0
sc-sigma                 = 0
couple-moltype           = Protein_chain_A   ; name of moleculetype to
couple-lambda0           = vdw              ;  only vdw interactions
couple-lambda1           = vdw-q            ; all interactions
couple-intramol          = no
nstdhdl                  = 10
; Generate velocities to start
gen_vel                  = no
; options for bonds
constraints              = none  ; we only have C-H bonds here
; Type of constraint algorithm
constraint-algorithm     = lincs
; Do not constrain the starting configuration
continuation             = no
; Highest order in the expansion of the constraint coupling matrix
lincs-order              = 12

Thank you in advance!!

Sonia Aguilera
Graduate assistant
Chemical Engineering Department
Universidad de los Andes

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