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
On Fri, 28 Mar 2008 David van der Spoel wrote :
JMandumpal wrote:
Dear list,
These are the energy I obtained running 60ps NVE of 500
TIP5P water molecules- I still wonder why the energy has not been
converged even having run for 160 ps in total (100 NVT + 60 NVE).
it is difficult to run NVE.
what constraint settings etc. do you use and what cutoffs.
100.000000 -15887.623027
101.500000 -15887.961065
103.000000 -15894.289055
104.500000 -15898.915859
106.000000 -15903.562196
107.500000 -15906.540627
109.000000 -15912.662455
110.500000 -15915.571468
112.000000 -15917.889520
113.500000 -15923.955612
115.000000 -15929.135491
116.500000 -15932.507824
118.000000 -15937.882055
119.500000 -15941.562218
121.000000 -15945.644608
122.500000 -15949.063632
124.000000 -15953.389791
125.500000 -15957.524802
127.000000 -15962.299775
128.500000 -15967.579640
130.000000 -15972.576889
131.500000 -15975.427574
133.000000 -15980.852975
134.500000 -15985.584201
136.000000 -15988.488715
137.500000 -15993.295989
139.000000 -15997.867767
140.500000 -16000.630051
142.000000 -16005.100451
143.500000 -16009.649201
145.000000 -16014.842764
146.500000 -16019.498233
148.000000 -16022.975477
149.500000 -16027.677441
151.000000 -16032.965475
152.500000 -16036.043976
154.000000 -16039.844112
155.500000 -16044.836132
157.000000 -16047.992186
158.500000 -16052.196926
160.000000 -16056.946593
-----------------------
I corrected these variables to:
tinit = 100
init_step = 0
Where could be the problem, then? Or should I run for even longer?
regards,
Jes
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