[gmx-users] How to run MD with longer recording interval to reduce the file size?

Qinghua Liao scorpio.liao at gmail.com
Fri Dec 15 13:13:49 CET 2017


Hello,

Normally, you don't need to write out the force and velocity, then you 
can set nstfout and nstvout as ZERO, then only
the coordinates will be written out in a xtc file.

If you don't care about waters, then you can also set xtc-grps as a 
group without waters and counterions.

Best,
Qinghua

On 12/15/2017 11:33 AM, ZHANG Cheng wrote:
> Dear Gromacs,
> I am following Justin's tutorial of "Lysozyme in Water" to run the MD.
>
>
> The .trr file got more than 10 GB after 30 ns. So I plan to run a MD with less frequent intervals.
>
>
> In the md.mdp file, the "dt = 0.002". My understanding is to change the five "5000" into "50000" to achieve 10 times less file size:
>
>
> i.e. change the following
> nstxout		        = 5000
> nstvout		        = 5000
> nstenergy	        = 5000
> nstlog		        = 5000
> nstxout-compressed  = 5000
>
>
>
> into
>
>
> nstxout		        = 50000
> nstvout		        = 50000
> nstenergy	        = 50000
> nstlog		        = 50000
> nstxout-compressed  = 50000
>
>
>
> Can I ask, if there is something else I need to do in addition to those five "5000"?
>
>
> Thank you.
>
>
> Yours sincerely
> Cheng



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