[gmx-users] affect of water removal on subsequent energy calculations

Alex nedomacho at gmail.com
Wed Apr 11 09:51:34 CEST 2018

If you plan to extract anything explicitly related to water from your 
reruns -- very much so. Basically unusable trajectories.


On 4/11/2018 1:48 AM, Harry Mark Greenblatt wrote:
> B”SD
> In an effort to reduce the size of output xtc files of simulations of large systems, we thought of saving these files without water molecules.
>    It occurred to us, however, that upon subsequent cpu-only reruns in order to do energy calculations, these results would be adversely affected, since the water molecules are not stored in the xtc file.
> Is this indeed a concern?
> Thanks
> Harry
> --------------------------------------------------------------------
> Harry M. Greenblatt
> Associate Staff Scientist
> Dept of Structural Biology           harry.greenblatt at weizmann.ac.il<../../owa/redir.aspx?C=QQgUExlE8Ueu2zs5OGxuL5gubHf97c8IyXxHOfOIqyzCgIQtXppXx1YBYaN5yrHbaDn2xAb8moU.&URL=mailto%3aharry.greenblatt%40weizmann.ac.il>
> Weizmann Institute of Science        Phone:  972-8-934-6340
> 234 Herzl St.                        Facsimile:   972-8-934-3361
> Rehovot, 7610001
> Israel

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