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 
<nedoma...@gmail.com<mailto:nedoma...@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
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Harry M. Greenblatt
Associate Staff Scientist
Dept of Structural Biology           
harry.greenbl...@weizmann.ac.il<../../owa/redir.aspx?C=QQgUExlE8Ueu2zs5OGxuL5gubHf97c8IyXxHOfOIqyzCgIQtXppXx1YBYaN5yrHbaDn2xAb8moU.&URL=mailto%3aharry.greenblatt%40weizmann.ac.il>
Weizmann Institute of Science        Phone:  972-8-934-6340
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