[gmx-users] heat apears

[Nguyen Hoang Phuong]

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.
>
>
> --
> Groetjes,
>
> Anton

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.

Phuong