[gmx-users] Note on oscillation period / time step

[Robin C. Underwood]

GMX Users:

When I run grompp on methanol in water in v. 4.5.3 I get the following Note:

NOTE 1 [file methanol.top, line 73]:
  The bond in molecule-type MET between atoms 5 OA and 6 HO has an
  estimated oscillational period of 9.0e-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:

;	User Robin
;	Wed Dec.1 2010
;	Input file
;
title               =  Yo
cpp                 =  /lib/cpp
integrator          =  md
dt                  =  0.001	; ps !
nsteps              =  1100000	; total 1000 ps=1 ns
nstcomm             =  10
; (x) coordinates, (v) is velocities, (f) is forces
; This affects "traj.trr" 
; these numbers shouldn't be too small (100,000), takes up disk space
nstxout             =  1000
nstvout             =  1000
nstfout             =  1000
; Output frequency for energies
nstlog              =  100
nstenergy           =  100
; This affects ".xtc" file for movies this should be a fairly small number
nstxtcout           =  100
xtc-precision       =  1000
; parameters for neighbors
nstlist             =  10
ns_type             =  grid
rlist               =  0.9
; electrostatics
coulombtype	    =  pme
pme_order	    =  4
ewald_rtol 	    =  1e-5
ewald_geometry      =  3d
epsilon_surface     =  0
fourierspacing	    =  0.1
fourier_nx          =  0.0
fourier_ny          =  0.0
fourier_nz          =  0.0
rcoulomb            =  0.9
optimize_fft        =  yes
Dispcorr	    =  EnerPres
vdwtype		    =  cutoff
rvdw_switch	    =  0.85
rvdw                =  0.9
; Berendsen temperature coupling is on in two groups
Tcoupl              =  v_rescale
tc-grps		    =  system
tau_t               =  0.1
ref_t               =  300
; Energy monitoring
energygrps          =  MET  SOL
; Isotropic pressure coupling is now on
Pcoupl              =  berendsen
Pcoupltype          = isotropic
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites is off at 300 K.
gen_vel             =  no
gen_temp            =  300.0
gen_seed            =  173529


Here is my top file:

;
;
; Include forcefield parameters
#include "ffoplsaa.itp"

;
; Methanol, Jorgensen et al. JACS 118 pp. 11225 (1996)
;
[ moleculetype ]
; name  nrexcl
MET	3

[ atoms ]
;   nr    type   resnr  residu    atom    cgnr        charge          mass
     1       opls_157       1     MET        C       1	0.145	 
     2       opls_156       1     MET        H       1	0.04	
     3       opls_156       1     MET        H       1	0.04	
     4       opls_156       1     MET        H       1	0.04	
     5       opls_154       1     MET       OA       1	-0.683 
     6       opls_155       1     MET       HO       1	0.418
   
[ bonds ]
;  ai    aj funct           c0           c1
1	2	1
1	3	1
1	4	1 
1	5	1
5	6	1
 
[ pairs ]
; i	j	funct
2	6
3	6
4	6

[ angles ]
;  ai    aj    ak funct           c0        c1
; H3
 2	1	5	1
 3	1	5 	1 
 4	1	5	1
 4      1       3 	1
 4	1	2	1


[ system ]
; Name
MET in water

[ molecules ]
; Compound        #mols
MET               1
SOL		503


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

Thanks,
Robin


-- 
Robin C. Underwood
Chemistry Department
560 Oval Drive
West Lafayette, IN 47907