[gmx-users] Bad energy conservation.

[Ram'on Garc'ia Fern'andez]

On Thu, Dec 05, 2002 at 03:38:11PM +0100, David van der Spoel wrote:
> > With 'cut-off' and rvdw < rlist, an increase in rvdw does not modify the energy.
> > This is a counterintuitive behaviour.
> > 
> no because interaction are computed up until rvdw only.

I have just tested it and confirmed that with rvdw < rlist, the value of rvdw
does not make any difference.

My tests have been made for a box of lennard-jones diatomic molecules.
vdwtype = Cut-Off

(1) rlist = 3.0, rvdw = 2.5
(2) rlist = 3.0, rvdw = 2.9

The energies are exactly the same.

I am attaching the input and log files. I am attaching only one
of the mdp files, the other is trivial to deduce. You can look
at the log files to see if I overlooked something.
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; Reproducci?n de la simulaci?n de J. Chem. Phys 116(17), pg 7649, 1 mayo 2002
; C. Vega, F. J. Blas, A. Galindo, "Extending Wertheim perturbation theory to
; the solid phase of the Lennard-Jones chains: Determination of the global 
; phase diagram"

; T* = 2, rho*=0.3226, L*=1, 432 mol?culas

[defaults]
; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
  1             1               no              0.0     0.0

[atomtypes]
; atom type; m (u); q (e);   particle type; c6;        c12
X           35.353  0        A             4          4

[constrainttypes]
X   X   1 1

[angletypes]
; i    j    k func       th0         cth


[dihedraltypes]


[nonbond_params]
; i    j   func    c6       c12
; Emacs lisp code for evaluating c6 and c12 from sigma and epsilon
; (defun c6c12 (sigma epsilon) (list (* 4 epsilon (expt sigma 6)) (* 4 epsilon (expt sigma 12))))
; sigma = 1, epsilon = 1
X   X         1    4 4

[moleculetype]
dimer 1

[atoms]
;    nr    type    resnr residu    atom    cgnr charge
      1       X   1      chlorine   X1   1
      2       X   1      chlorine   X2   2

[constraints]
      1  2 1

[angles]
; ai    aj    ak funct    th0    cth


[dihedrals]

[system]
dimer system, 432 molecules

[molecules]
dimer 432
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;
;       Input file
;
title               =  "Dimer"                  ; a string
dt                  =  0.01                   ; time step
integrator          =  md
nsteps              =  100                      ; number of steps
nstcomm             =  1                        ; reset c.o.m. motion
; output options
nstxout             =  100                      ; write coords
nstvout             =  100                      ; write velocities
nstlog              =  10                       ; print to logfile
nstenergy           =  10                       ; print energies
nstfout             =  100
; vdw-coul optins
nstlist             =  40                       ; update pairlist
ns_type             =  grid                     ; pairlist method
rlist               =  3.0                      ; cut-off for ns
rvdw                =  2.9                      ; cut-off for vdw
rcoulomb            =  2.9                      ; cut-off for coulomb
vdwtype             =  cut-off
coulombtype         =  cut-off

; simulation type options
tcoupl              =  no                       ; temperature coupling
Pcoupl              =  no                       ; pressure bath
gen_vel             =  no                       ; generate initial velocities
unconstrained-start = no
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