[gmx-users] heat apears
Nguyen Hoang Phuong
phuong at theochem.uni-frankfurt.de
Mon Dec 1 09:01:01 CET 2003
On Mon, 1 Dec 2003, Anton Feenstra wrote:
> David van der Spoel wrote:
> > On Fri, 28 Nov 2003 parinald at unsl.edu.ar wrote:
> >>Thank ´s Dallas and Anton:
> >> Now I run g_energy to analyze temperature, presure and volume,
> >>started the simulation at 300 K and the size of the box was (2.5 2 2).
> >>My .mdp file is:
> >>cpp = /lib/cpp
> >>constraints = all-bonds
> >>integrator = md
> >>dt = 0.002 ; ps !
> >>nsteps = 500000 ; total 1000 ps.
> >>nstcomm = 1
> >>nstxout = 250
> >>nstvout = 1000
> >>nstfout = 0
> >>nstlog = 100
> >>nstenergy = 100
> >>nstlist = 10
> >>ns_type = grid
> >>rlist = 0.5
> >>rcoulomb = 0.5
> >>rvdw = 0.5
> > your cut-offs are too short. Make it 1 nm.
> Or, rather, try a twin-range, like rlist=0.8, rcoulomb=1.2, rvwd=1.2.
> For something like ATP with ions, you may want PME in stead of a cut-off.
> Finally, be aware that temperature often can be a few degrees above
> 'ref_t', and that pressure fluctuations are *huge*, indeed as you already
> saw they are on the order of 1000's of bar. The average pressure should
> still be very close to 1, after a few 100ps.
just a comment: before I used rlist=0.9, rcoulomb=1.2, rvwd=1.2 to
simulate the water system, the temperature increased about 5-10K. If all
the cutoffs are the same (e.g rlist=1.2, rcoulomb=1.2, rvwd=1.2) I got the
right temperature ref_t.
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