[gmx-users] constraint

[NIKHIL JOSHI]

GMX Users:

When I run grompp on Polyetylene Oxide in water, I get the following Note:

NOTE 2 [file topol-trappeR-B.top, line 423]:
  The bond in molecule-type PEO between atoms 2 O12 and 3 C23 has an
  estimated oscillational period of 6.0e-03 ps, which is less than 10 times
  the time step of 1.0e-03 ps.
  Maybe you forgot to change the constraints mdp option.

Here is my mdp file

; RUN CONTROL PARAMETERS
integrator               = md

; Start time and timestep in ps
dt                       = 0.002  ; 2 fs
nsteps                   = 250000 ; 5 ns

; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout                  = 0 ;
nstvout                  = 0 ;
nstlog                   = 500   ; 1ps
nstenergy                = 500 ; 1 ps
nstxtcout                = 500 ; 1ps
xtc-precision            = 1000
xtc-grps                 = System

; ENERGY EXCLUSION
energygrps = System
;comm_mode = none
;nstcomm = 1000000

; BOUNDARY CONDITIONS
pbc                      = xyz

; NEIGHBOR SEARCHING PARAMETERS
cutoff-scheme     = Verlet
nstlist                  = 40
ns_type                  = grid
rlist                    = 1.0

; Method for doing Van der Waals
vdwtype                  = Cut-off
rvdw                     = 1.0

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype              = PME
rcoulomb                 = 1.0

; Spacing for the PME/PPPM FFT grid
fourierspacing           = 0.12

; EWALD/PME/PPPM parameters
pme_order                = 4
ewald_rtol               = 1e-05
ewald_geometry           = 3d
epsilon_surface          = 0
optimize_fft             = no


; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
Tcoupl                   = nose-hoover
tc-grps                  = System
tau_t                    = 2.5
ref_t                    = 300
; Pressure coupling
;Pcoupl                   = Parrinello-Rahman
;Pcoupltype               = Isotropic
;tau_p                    = 5.0
;ref_p                    = 1.0
;compressibility          = 4.5e-05

; OPTIONS FOR BONDS
constraints              = h-bonds
constraint_algorithm     = SHAKE
; Relative tolerance of shake
;shake-tol                = 1e-04

Here is my top file:
; SINGLE CHAIN PEO [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ
fudgeQQ 1 2 no [ atomtypes ] ; name at.num mass charge ptype sigma epsilon
(TRAPPE MODEL) OW 15.99940 -0.8476 A 3.16557e-01 6.50194e-01 HW 1.00800
0.4238 A 0.00000e+00 0.00000e+00 C2 14.02700 +0.250 A 3.95000e-01
3.82467e-01 C3 15.03500 +0.250 A 3.75000e-01 8.14821e-01 O1 15.99940 -0.500
A 2.80000e-01 4.57000e-01 [ bondtypes ] ;i j func b0 kb OW HW 1 0.100
345000 HW HW 1 0.16330 345000 C2 C2 1 0.15400 376000 C3 O1 1 0.14100 267900
C2 O1 1 0.14100 267900 [ angletypes ] ;i j k func th0 cth C2 O1 C2 1 112
519.6 C3 C2 O1 1 112 418.2 [ dihedraltypes ] ;i j k l func c0 c1 c2 c3 c4
c5 (kJ/mol) C3 O1 C2 C2 3 -5.1599 -0.6971 5.35013 0.80312 0.28307 0.09526
O1 C2 C2 O1 3 7.58526 6.70523 8.40071 0.63221 0.11063 0.35962 C2 C2 O1 C3 3
-5.1599 -0.6971 5.35013 0.80312 0.28307 0.09526 [ moleculetype ] PEO 3 [
atoms ] ; nr type resnr residue atom cgnr charge 1 C3 1 PEO C31 1 0 2 O1 1
PEO O12 1 0 3 C2 1 PEO C23 1 0 4 C2 1 PEO C24 2 0 5 O1 1 PEO O15 2 0 6 C2 1
PEO C26 2 0 7 C2 1 PEO C27 3 0 8 O1 1 PEO O18 3 0 9 C2 1 PEO C29 3 0 10 C2
1 PEO C210 4 0 11 O1 1 PEO O111 4 0 12 C2 1 PEO C212 4 0 13 C2 1 PEO C213 5
0 14 O1 1 PEO O114 5 0 15 C3 1 PEO C315 6 0 [ bonds ] ;i j funct length
force.c 1 2 1 0.141 8180000 2 3 1 0.141 8180000 3 4 1 0.154 7150000 4 5 1
0.141 8180000 5 6 1 0.141 8180000 6 7 1 0.154 7150000 7 8 1 0.141 8180000 8
9 1 0.141 8180000 9 10 1 0.154 7150000 10 11 1 0.141 8180000 [ angles ] ; i
j k funct theta force.c 1 2 3 1 112 519.6 2 3 4 1 112 418.2 3 4 5 1 112
418.2 4 5 6 1 112 519.6 5 6 7 1 112 418.2 6 7 8 1 112 418.2 7 8 9 1 112
519.6 8 9 10 1 112 418.2 9 10 11 1 112 418.2 10 11 12 1 112 519.6 [
dihedrals ] ;i j k l func c0 c1 c2 c3 c4 c5 1 2 3 4 3 -5.15997 -0.69711
5.35013 0.80312 0.28307 0.09526 2 3 4 5 3 7.58526 6.70523 8.40071 0.63221
0.11063 0.35962 3 4 5 6 3 -5.15997 -0.69711 5.35013 0.80312 0.28307 0.09526
4 5 6 7 3 -5.15997 -0.69711 5.35013 0.80312 0.28307 0.09526 5 6 7 8 3
7.58526 6.70523 8.40071 0.63221 0.11063 0.35962 6 7 8 9 3 -5.15997 -0.69711
5.35013 0.80312 0.28307 0.09526 7 8 9 10 3 -5.15997 -0.69711 5.35013
0.80312 0.28307 0.09526 8 9 10 11 3 7.58526 6.70523 8.40071 0.63221 0.11063
0.35962 9 10 11 12 3 -5.15997 -0.69711 5.35013 0.80312 0.28307 0.09526 [
moleculetype ] ;molname nrexcl SOL 2 [ atoms ] ; nr type resnr residue atom
cgnr charge mass 1 OW 1 SOL OW 1 -0.8476 2 HW 1 SOL HW1 1 0.4238 3 HW 1 SOL
HW2 1 0.4238 [ bonds ] ; i j funct length force.c. 1 2 1 0.10000 345000 1 3
1 0.10000 345000 2 3 1 0.16330 345000 [ system ] PEO-SINGLECHAIN [
molecules ] PEO 1

Do I need to add some sort of constraint on my methanol molecule?

Thanks,
Nik