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

[Harry Mark Greenblatt]

BS”D

 Dear Alex,

  Not *explicitly* related to water:  we would like to look at interaction energies between parts of proteins, or proteins and DNA.  So screening comes to mind…


Harry


On 11 Apr 2018, at 10:51 AM, Alex <nedomacho at gmail.com<mailto:nedomacho at gmail.com>> wrote:

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

Alex


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



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Harry M. Greenblatt
Associate Staff Scientist
Dept of Structural Biology           harry.greenblatt at weizmann.ac.il<mailto:harry.greenblatt at weizmann.ac.il><../../owa/redir.aspx?C=QQgUExlE8Ueu2zs5OGxuL5gubHf97c8IyXxHOfOIqyzCgIQtXppXx1YBYaN5yrHbaDn2xAb8moU.&URL=mailto%3aharry.greenblatt%40weizmann.ac.il<http://40weizmann.ac.il/>>
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--------------------------------------------------------------------
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