On 6/24/13 1:07 PM, Sonia Aguilera wrote:
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
decouple
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
The problem almost certainly comes from the use of "couple-intramol = no," which
for large molecules can cause issues (which have been reported before). Larger
molecules are more flexible, and thus the interaction distances can vary a lot.
The manual suggests using "couple-intramol = yes" for large molecules.
Whether or not this is an appropriate setting for whatever you're trying to do
is up to you and perhaps table-extension could be increased in this case, as it
is not likely a crash but also something you cannot simply ignore.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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