[gmx-users] gromacs.org_gmx-users Digest, Vol 167, Issue 53
jojo412202 at gmail.com
Tue Mar 13 18:28:10 CET 2018
I have looked in the manual and tried the adjustments for
verlet-buffer-tolerance and rlist (with no sucess), but I did not find a
plot for this? Can you direct me to this? I've copied my mdp below if
anyone could give me some insight.
integrator = md
tinit = 0
dt = 0.001
nsteps = 10000000
comm-mode = Linear
nstcomm = 100
nstlog = 50000
nstenergy = 10000
nstcalcenergy = 100
nstxout-compressed = 1000
compressed-x-precision = 1000
; NEIGHBORLIST PARAMETERS
cutoff-scheme = Verlet
nstlist = 10
ns_type = grid
pbc = xyz
verlet-buffer-tolerance = 5.0e-6 ;-1
; VDW AND COULOMB PARAMETERS
coulombtype = PME
rcoulomb = 0.9
coulomb-modifier = Potential-shift
vdw-type = Cut-off
rvdw = 0.9
vdw-modifier = Potential-shift
table-extension = 1
; EWALD PARAMETERS
fourierspacing = 0.1
pme_order = 6
ewald_rtol = 1e-06
ewald_geometry = 3d
epsilon_surface = 0
DispCorr = EnerPres
; BAROSTAT AND THERMOSTAT
Tcoupl = no ;Nose-hoover
Pcoupl = no ;Parrinello-Rahman
refcoord-scaling = no
gen_vel = no
gen_temp = 298.15
gen_seed = -1
> Message: 5
> Date: Mon, 12 Mar 2018 22:20:45 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] nve simulation
> <CAMNuMAQ-j7HN-Hz_UJ9CRKmirG=wbsMwSLQZT42_h=tui_mHUQ at mail.
> Content-Type: text/plain; charset="UTF-8"
> The list can't accept attachments.
> There's a plot in the reference manual that shows some indicative minimal
> drifts, which would be a good place to search. :-)
> On Mon, Mar 12, 2018 at 9:31 PM Jo <jojo412202 at gmail.com> wrote:
> > Hello,
> > I would like to run an NVE simulation but am having trouble conserving
> > energy. From some past postings on the email list, I understand that
> > neighborlist buffer parameters need to be adjusted, however I still am
> > able to conserve energy. I am simulating a box of 1000 SPCE water, and I
> > also suspect 'settles' could be causing the lack of energy conservation.
> > Can anyone provide any suggestions on what I can do to conserve energy?
> > have attached the mdp file.
> > Thank you,
> > Jo
> > --
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> End of gromacs.org_gmx-users Digest, Vol 167, Issue 53
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