Hi Jes,
if you want just to do NVE, it should, in my opinion,
work also with the Cut-off. But it should also work with
the Shift, and then your potential will be smooth and
nice, so this might be the choice you want to take.
The information given in 7.3.10 is quite cryptic,
and you can see more about what the different cut-
offs mean in Gromacs from for example here:
http://www.gromacs.org/pipermail/gmx-users/2007-July/028626.html
The bottom line being, though, that if you want to do
things correct, you set rvdw < rlist. All this wizardry
with twin range cut-offs and setting rlist < rvdw will
not work in NVE, because you will not have the thermostat
to fix the errors done in the integration.
Cheers,
markus.
--
Halli delendum est.
On Apr 7, 2008, at 02:26 , [EMAIL PROTECTED] wrote:
Date: 7 Apr 2008 03:52:42 -0000
From: "JMandumpal" <[EMAIL PROTECTED]>
Subject: Re: Re: Re: [gmx-users] NVT and NVE
To: "Discussion list for GROMACS users" <[email protected]>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset="iso-8859-1"
Hi Markus,
It means that I should change cutoff to the Shift, right (manual
7.3.10)
jes
On Sat, 05 Apr 2008 Markus Miettinen wrote :
Hi Jes,
to me it seems that you have rlist = rvdw:
nstlist = 10
rlist = 1.0
rvdw = 1.0
This will lead to a loss of energy, because between list updates
two particles originally at distance, say, 1.01 from each other
can easily move within rvdw from each other, but they will not
"see" each other until the lists are updated again.
In other words, you have particles moving within the attractive
LJ-potential region without giving them the speed-up that the
attractive potential should provide. This mistake equals loss of
energy, and becomes apparent in NVE. In NVT the thermostat
(artificially!) fixes the energy loss.
The correct way is to set rlist > rvdw.
Cheers,
markus.
--
Halli delendum est.
On Apr 3, 2008, at 13:00 , [EMAIL PROTECTED] wrote:
Date: 3 Apr 2008 08:12:40 -0000
From: "JMandumpal" <[EMAIL PROTECTED]>
Subject: Re: Re: [gmx-users] NVT and NVE
To: "Discussion list for GROMACS users" <[email protected]>
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain; charset="iso-8859-1"
Dear David,
I post the input file for the NVE run.
I use SHAKE, Would it be better if I use LINCS?
title = NVE
cpp = /usr/bin/cpp
; RUN CONTROL PARAMETERS
integrator = md
; Start time and timestep in ps
tinit = 500
dt = 0.0015;
nsteps = 360000; 540 ps
; For exact run continuation or redoing part of a run
init_step = 0
; number of steps for center of mass motion removal
nstcomm = 1
; group(s) for center of mass motion removal
comm-grps = SOL
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 0
nstvout = 0
nstfout = 0
; Checkpointing helps you continue after crashes
nstcheckpoint = 1000
; Output frequency for energies to log file and energy file
nstlog = 100000
nstenergy = 1000
; Output frequency and precision for xtc file
nstxtcout = 0
xtc-precision = 1000
; select multiple groups. By default all atoms will be written.
; NEIGHBORSEARCHING PARAMETERS
nstlist = 10
; ns algorithm (simple or grid)
ns_type = grid
; Periodic boundary conditions:
pbc = xyz
; nblist cut-off
rlist = 1.0
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = pme
rcoulomb = 1.0
ewald_rtol = 1e-5 ; since erfc(sigma*rcutoff)
=ewald_rtol
optimize_fft = yes
; Relative dielectric constant for the medium
epsilon_r = 1 ; for water
; Method for doing Van der Waals
vdw-type = cut-off
rvdw = 1.0
; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.12 ;
; EWALD/PME/PPPM parameters
pme_order = 4
ewald_geometry = 3d
epsilon_surface = 0
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
Tcoupl = no
Pcoupl = no
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = no
gen-temp = 300
gen-seed = 173529
; OPTIONS FOR BONDS
constraints = all-bonds
constraint_algorithm = shake
shake_tol = 0.0001
morse = no
rgds,
Jes
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