[gmx-users] gromacs.org_gmx-users Digest, Vol 167, Issue 53

[Jo]

Hello,

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.

Thanks,

Jo

RUN PARAMETERS
integrator               = md
tinit                    = 0
dt                       = 0.001
nsteps                   = 10000000
comm-mode                = Linear
nstcomm                  = 100

;OUTPUT PARAMETERS
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

;SETUP VELOCITIES=
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
> Message-ID:
>         <CAMNuMAQ-j7HN-Hz_UJ9CRKmirG=wbsMwSLQZT42_h=tui_mHUQ at mail.
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi,
>
> 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. :-)
>
> Mark
>
> 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
> the
> > energy.  From some past postings on the email list, I understand that
> some
> > neighborlist buffer parameters need to be adjusted, however I still am
> not
> > 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?
> I
> > have attached the mdp file.
> >
> > Thank you,
> >
> > Jo
> > --
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> End of gromacs.org_gmx-users Digest, Vol 167, Issue 53
> ******************************************************
>