<div>Robin,</div><div><br></div>Easiest way to get it running, with the flexible bond between O and H in methane would be to decrease the time step. I would start with half a femto second time step and see what happens.<div>
<br></div><div>All the best</div><div>Rajesh<br><br><div class="gmail_quote">On Thu, Dec 2, 2010 at 10:11 AM, Robin C. Underwood <span dir="ltr"><<a href="mailto:rcunderw@purdue.edu">rcunderw@purdue.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">GMX Users:<br>
<br>
When I run grompp on methanol in water in v. 4.5.3 I get the following Note:<br>
<br>
NOTE 1 [file methanol.top, line 73]:<br>
The bond in molecule-type MET between atoms 5 OA and 6 HO has an<br>
estimated oscillational period of 9.0e-03 ps, which is less than 10 times<br>
the time step of 1.0e-03 ps.<br>
Maybe you forgot to change the constraints mdp option.<br>
<br>
Here is my mdp file:<br>
<br>
; User Robin<br>
; Wed Dec.1 2010<br>
; Input file<br>
;<br>
title = Yo<br>
cpp = /lib/cpp<br>
integrator = md<br>
dt = 0.001 ; ps !<br>
nsteps = 1100000 ; total 1000 ps=1 ns<br>
nstcomm = 10<br>
; (x) coordinates, (v) is velocities, (f) is forces<br>
; This affects "traj.trr"<br>
; these numbers shouldn't be too small (100,000), takes up disk space<br>
nstxout = 1000<br>
nstvout = 1000<br>
nstfout = 1000<br>
; Output frequency for energies<br>
nstlog = 100<br>
nstenergy = 100<br>
; This affects ".xtc" file for movies this should be a fairly small number<br>
nstxtcout = 100<br>
xtc-precision = 1000<br>
; parameters for neighbors<br>
nstlist = 10<br>
ns_type = grid<br>
rlist = 0.9<br>
; electrostatics<br>
coulombtype = pme<br>
pme_order = 4<br>
ewald_rtol = 1e-5<br>
ewald_geometry = 3d<br>
epsilon_surface = 0<br>
fourierspacing = 0.1<br>
fourier_nx = 0.0<br>
fourier_ny = 0.0<br>
fourier_nz = 0.0<br>
rcoulomb = 0.9<br>
optimize_fft = yes<br>
Dispcorr = EnerPres<br>
vdwtype = cutoff<br>
rvdw_switch = 0.85<br>
rvdw = 0.9<br>
; Berendsen temperature coupling is on in two groups<br>
Tcoupl = v_rescale<br>
tc-grps = system<br>
tau_t = 0.1<br>
ref_t = 300<br>
; Energy monitoring<br>
energygrps = MET SOL<br>
; Isotropic pressure coupling is now on<br>
Pcoupl = berendsen<br>
Pcoupltype = isotropic<br>
tau_p = 0.5<br>
compressibility = 4.5e-5<br>
ref_p = 1.0<br>
; Generate velocites is off at 300 K.<br>
gen_vel = no<br>
gen_temp = 300.0<br>
gen_seed = 173529<br>
<br>
<br>
Here is my top file:<br>
<br>
;<br>
;<br>
; Include forcefield parameters<br>
#include "ffoplsaa.itp"<br>
<br>
;<br>
; Methanol, Jorgensen et al. JACS 118 pp. 11225 (1996)<br>
;<br>
[ moleculetype ]<br>
; name nrexcl<br>
MET 3<br>
<br>
[ atoms ]<br>
; nr type resnr residu atom cgnr charge mass<br>
1 opls_157 1 MET C 1 0.145<br>
2 opls_156 1 MET H 1 0.04<br>
3 opls_156 1 MET H 1 0.04<br>
4 opls_156 1 MET H 1 0.04<br>
5 opls_154 1 MET OA 1 -0.683<br>
6 opls_155 1 MET HO 1 0.418<br>
<br>
[ bonds ]<br>
; ai aj funct c0 c1<br>
1 2 1<br>
1 3 1<br>
1 4 1<br>
1 5 1<br>
5 6 1<br>
<br>
[ pairs ]<br>
; i j funct<br>
2 6<br>
3 6<br>
4 6<br>
<br>
[ angles ]<br>
; ai aj ak funct c0 c1<br>
; H3<br>
2 1 5 1<br>
3 1 5 1<br>
4 1 5 1<br>
4 1 3 1<br>
4 1 2 1<br>
<br>
<br>
[ system ]<br>
; Name<br>
MET in water<br>
<br>
[ molecules ]<br>
; Compound #mols<br>
MET 1<br>
SOL 503<br>
<br>
<br>
Do I need to add some sort of constraint on my methanol molecule?<br>
<br>
Thanks,<br>
Robin<br>
<br>
<br>
--<br>
Robin C. Underwood<br>
Chemistry Department<br>
560 Oval Drive<br>
West Lafayette, IN 47907<br>
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</font></blockquote></div><br><br clear="all"><br>-- <br>Naga Rajesh Tummala, PhD<br>School of Chemical, Biological, and Materials Engineering<br>University of Oklahoma<br><br><br>
</div>