[gmx-users] Imaging Problem

[Ilya Chorny]

Hello 

I ran a distance restraint calculation between two molecules where I
kept the distance between two of the atoms fixed. I had some strange
results and when I watched the trajectory using VMD I noticed that when
one of the molecules left the box it got moved to the other side as one
would expect but the distance between the molecules  also changed to the
geometric distance and not the min image distance. Am I making some
mistake in setting up the calculation.


Thanks

Ilya

cpp                 =  /lib/cpp
integrator          =  md
constraints         =  all-bonds
dt                  =  0.002    ; ps !
nsteps              =  500000     ; total 10 ps.
nstcomm             =  1
nstenergy           =  100
nstlist             =  1
coulombtype         =  PME
rlist               =  .9
rcoulomb            =  .9
rvdw                =  .9
Tcoupl              =  nose-hoover
tc-grps             =  SOL COO AGG
tau_t               =  0.1 0.1 .1
ref_t               =  300 300 300
; Energy monitoring
; Pressure coupling is not on
Pcoupl              =  berendsen
tau_p               =  0.5
compressibility     =  6.0e-6
ref_p               =  1.0
; Generate velocites is on at 300 K.
gen_vel             =  yes
gen_temp            =  300.0
gen_seed            =  173529
; distance restraints
disre               =  simple
disre_weighting     =  equal
nstdisreout         =  10