[gmx-users] Imaging Problem
ichorny at maxwell.compbio.ucsf.edu
Tue Nov 25 18:25:01 CET 2003
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?
On Mon, 2003-11-24 at 11:48, Ilya Chorny wrote:
> 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.
> 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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