[gmx-users] Re: Water models and diffusion coefficient

[Dr. Vitaly Chaban]

> For a simulation that is 300 ns long (after NVT and NPT equilibration steps
> of 1 ns each), I am saving output every 2 ps. The time step is 2 fs.
>
> nstxout         = 1000          ; save coordinates every 2 ps
> nstvout         = 1000          ; save velocities every 2 ps
> nstxtcout       = 1000          ; xtc compressed trajectory output every 2
> ps
> nstenergy       = 1000          ; save energies every 2 ps
> nstlog          = 1000          ; update log file every 2 ps
>
> Is that saving data too rarely?
>
> Thanks,
>
>
>
>
> --
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>
>
> ------------------------------
>
> Message: 4
> Date: Sat, 09 Feb 2013 19:58:04 +0100
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] Re: Water models and diffusion coefficient
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <51169C3C.8020101 at xray.bmc.uu.se>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> On 2013-02-09 19:26, learnmd wrote:
>> For a simulation that is 300 ns long (after NVT and NPT equilibration steps
>> of 1 ns each), I am saving output every 2 ps. The time step is 2 fs.
>>
>> nstxout         = 1000          ; save coordinates every 2 ps
>> nstvout         = 1000          ; save velocities every 2 ps
>> nstxtcout       = 1000          ; xtc compressed trajectory output every 2
>> ps
>> nstenergy       = 1000          ; save energies every 2 ps
>> nstlog          = 1000          ; update log file every 2 ps
>>
>> Is that saving data too rarely?
>>

I personally save every 100-500fs depending on the system.

There is not need in 300ns trajectory to get diffusion. 1ns is pretty enough.





Dr. Vitaly V. Chaban
MEMPHYS - Center for Biomembrane Physics
Department of Physics, Chemistry and Pharmacy
University of Southern Denmark
Campusvej 55, 5230 Odense M, Denmark