Javier Cerezo wrote:
Hello.
It looks like you're missing the bonded-interactions parameters.
[ bonds ]
; ai aj funct *R0 Kb
*1 2 1 * X X*
1 3 1 * X X*
1 4 1 * X X*
1 5 1 * X X*
5 6 1 * X X*
(also angles...)
Is it implicit somewhere? I don't know if it is automatic and if so,
from where the parameters are taken. If it is by using atoms names and
the ffbonded.itp from oplsaa, then atom name OA is missing in the itp file.
I think that, according to the code (grompp.c), this note may arise if
the force constants are zero.
Atom types are interpolated from ffbonded.itp and assigned. If the problem were
in the bonded parameters, a very different fatal error arises. There is no
problem here.
-Justin
Javier
El 02/12/10 17:11, Robin C. Underwood escribió:
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
--
Javier CEREZO BASTIDA
Estudiante de Doctorado
---------------------
Dpto. Química-Física
Universidad de Murcia
30100 MURCIA (España)
Tlf.(+34)868887434
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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