On 1/17/20 3:01 AM, Berk Hess wrote:
Hi,
Using center of mass motion removal in combination with an absolute reference
in the system, such as position restraints, will always lead to artifacts, as
physical motion is removed and not drift due to numerical rounding errors. For
the most common case of equilibrating macromolecules using position restraints
these artifacts are usually negligible.
So we should probably add a sentence to the note:
Removing center of mass motion in the presence of positions restraints might
cause artifacts. When position restraints are used to equilibrate a
macromolecule these artifacts are usually negligible.
Thanks, Berk. I do think this addition would be important. Most people
are going to encounter the note doing exactly what you describe,
equilibrating a macromolecule. If the artifacts are negligible in this
case, it should be made clear to avoid concern.
-Justin
I think we should add a comm-removal setting "auto" which should be the
default, so grompp can automatically turn off comm-removal when using position restraints.
I realize now that we should check if there are no other artifacts when doing
equilibration with position restraints in an NPT ensemble without comm-removal.
I expect NVT should be fine without comm-removal.
Cheers,
Berk
________________________________
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Christos Deligkaris
<deligka...@gmail.com>
Sent: Thursday, January 16, 2020 5:03 PM
To: gmx-us...@gromacs.org <gmx-us...@gromacs.org>
Subject: Re: [gmx-users] com motion and position restraints may cause artifacts
The ambiguity in the gromacs 2020 note made me concerned, as it was
not clear to me whether my system (DNA+small molecule) fills in the
category where artifacts are caused. The gromacs note could have been
a bit more helpful by referencing specific publications so that we can
educate ourselves.....
Best wishes,
Christos Deligkaris, PhD
On Thu, Jan 16, 2020 at 5:21 AM Justin Lemkul <jalem...@vt.edu> wrote:
On 1/16/20 5:17 AM, Alessandra Villa wrote:
Hi,
On Mon, Jan 13, 2020 at 3:36 PM Christos Deligkaris <deligka...@gmail.com>
wrote:
dear all,
I installed gromacs 2020 and I now get the following message during
equilibration:
NOTE 1 [file nvt.mdp]:
Removing center of mass motion in the presence of position
restraints might cause artifacts
I do not recall seeing this with gromacs 2018. In which cases are
artifacts created? Is it now recommended to not remove the center of
mass motion during equilibration?
It is recommended not to have position restrain and remove of center of
mass at the same moment. That is also the case of the equilibration phase.
That may cause artifact depending on the system and the condition you are
simulating.
What is the nature of these artifacts and where is this documented?
Combining position restraints with COM motion removal is an extremely
common practice. Phrases like "might cause artifacts" are troubling
because that implies uncertainty. Are there cases when this combination
does not cause artifacts?
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
--
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.
--
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.
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
--
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.
