[gmx-users] Re: viscosity and acflen in g_energy

David van der Spoel spoel at xray.bmc.uu.se
Mon Sep 28 07:09:05 CEST 2009

Mark Abraham wrote:
> Vitaly V. Chaban wrote:
>> Mark,
>> In "g_energy -h" I see nothing abous viscosity except the option
>> "-vis". The command line is as I  wrote earlier:
>> "g_energy -vis -acflen 1001"
>> The system is liquid water. The simulation time is 2 000 ps. The file
>> I look into is enecorr.xvg.
>> What the error of some sort do you mean?
> -acflen is measured in trajectory frames. How many relevant frames exist 
> in the trajectory file?

Viscosity in g_energy is computed from the pressure tensor which is 
stored in the energy file. Unfortunately is seems like the acflen is 
ignored in this case. Please submit a bugzilla.

On the other hand you need all the data you can get for this quantity, 
because it converges extremely slowly.

> Mark
>> Vitaly
>>>> When using g_energy to calculate viscosity ("g_energy -vis"), in
>>>> enecorr.xvg the ACF of stress tensor is output. How can one specify
>>>> the "acflen" of this ACF?
>>>> I try the key "g_energy -vis -acflen XXX" but the length of the ACF is
>>>> still equal to the half of the trajectory length.
>>> If you read g_energy -h, you will need to specify the ACF length in a
>>> particular way. If you'd given us your actual command line and some
>>> information about your trajectory, you might have gotten a definitive
>>> answer... as it is, we can only assume you made an error of some 
>>> sort! :-)
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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