From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Tue Jan 17 2012 - 07:03:36 CST
Dear Anonymous (Btw, is there a special reason for the anonymity?),
The pressure fluctuations are due to the finite size of the system (as
given by statistical mechanics). So if the system is small I would say this
is normal. I believe this has been discusses a lot on this mailing list in
the past.
Also, I don't think you need to use constant area for a water simulation.
Best regards,
Ajasja
On Tue, Jan 17, 2012 at 13:32, Namd Namd <namd_10_at_yahoo.com> wrote:
> Dear namd people,
>
> I performed 5 ns md simulation for water molecules in NPT ensamble to
> equilibrate the system. Target pressure is 1 atm and the values in conf
> file are
>
> # Constant Temperature Control
> langevin on
> langevinDamping 5
> langevinTemp $temperature
> langevinHydrogen on
>
>
> # Constant Pressure Control (variable volume)
> useGroupPressure no
> useFlexibleCell yes
> useConstantArea yes
>
> langevinPiston on
> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
> langevinPistonPeriod 200.
> langevinPistonDecay 100.
> langevinPistonTemp $temperature
>
>
> I found the density of water to be 1 g/cm3 but I couldnt reach the
> target pressure value. The pressure vs timestep graph file is in attached
> and fluctuation is too high. Could you please explain the reason of it ?
> What should I do also to reach the target pressure value ( 1 atm ) ?
>
> Best regards.
>
>
>
>
>
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