[gmx-users] Imaging Problem

[Ilya Chorny]

Could someone please take a look at my posting. I am attempting to do
umbrella sampling but this is a bug that was supposed to be fixed
according to the postings. Should I download the CVS version of gromacs?

Ilya


On Mon, 2003-11-24 at 11:48, Ilya Chorny wrote:
> 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
> 
> 
> 
> 
> 
> 
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