Screening effects in Gromacs come in a rather non-straightforward manner in terms of data extraction: they certainly exist within the simulations in the form of the fields induced by local water orientation, but to extract them from reruns is extremely challenging even if you're outputting water trajectories. If this is about interactions between different parts of proteins, I would absolutely output water trajectories, because otherwise you're left with LJ+electrostatics and assumptions on local dielectric constant, which in itself is a very nuanced problem: https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.99.077801

We're faced with very similar challenges at the moment, so we're independently postprocessing complete trajectories (including everything) and solving Poisson's eqn all over again to give e.g. time-averaged 3D electrostatics maps.

Alex


On 4/11/2018 1:56 AM, Harry Mark Greenblatt wrote:
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



--------------------------------------------------------------------
Harry M. Greenblatt
Associate Staff Scientist
Dept of Structural Biology           
harry.greenbl...@weizmann.ac.il<mailto:harry.greenbl...@weizmann.ac.il><../../owa/redir.aspx?C=QQgUExlE8Ueu2zs5OGxuL5gubHf97c8IyXxHOfOIqyzCgIQtXppXx1YBYaN5yrHbaDn2xAb8moU.&URL=mailto%3aharry.greenblatt%40weizmann.ac.il<http://40weizmann.ac.il/>>
Weizmann Institute of Science        Phone:  972-8-934-6340
234 Herzl St.                        Facsimile:   972-8-934-3361
Rehovot, 7610001
Israel


--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to 
gmx-users-requ...@gromacs.org<mailto:gmx-users-requ...@gromacs.org>.


--------------------------------------------------------------------
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
234 Herzl St.                        Facsimile:   972-8-934-3361
Rehovot, 7610001
Israel


--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Reply via email to