[gmx-users] Reduced LJ Units

[Sai Pooja]

Thanks Mark. I looked at the link you has sent. However, with pressure
coupling I haven't seen such fluctuations for my system. The pressure value
is the one obtained at the end of a long NPT simulation - 10^8 steps with
dt=10^-4. The rms fluctuations in  pressure are small, of the order of 1-0.1
bar.


On Tue, Jun 8, 2010 at 6:34 PM, Mark Abraham <mark.abraham at anu.edu.au>wrote:

> ----- Original Message -----
> From: Sai Pooja <saipooja at gmail.com>
> Date: Wednesday, June 9, 2010 8:07
> Subject: [gmx-users] Reduced LJ Units
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>
> > Hi,
>
> > I have trouble searching mailing lists so I apologize if this has
> already been answered in some query.
> >
> > If sigma=epsilon=mass=1 is specified in .top file then for specifying
>  T*=1 in the Thermostat does one need to set ref_t ~ 120 ?
> >
> > Similarly, to specify ref_p for the Barostat, is there a similar
> conversion factor?
> >
> > How about the values of P reported in bar? How does one convert that to
> reduced units?
>
> Does manual table 2.4 help?
>
>
> > I ask this because I have currently specified ref_t =120 as explained in
> the Gromacs manual. However this gives me a pressure value(in bars) which is
> much much larger than the one I had expected in reduced units (by a factor
> of about 50-60).
>
> Are you measuring pressure over long enough time? See
> http://www.gromacs.org/Documentation/Terminology/Pressure
>
> Mark
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-- 
Quaerendo Invenietis-Seek and you shall discover.
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