On 3/12/18 9:48 AM, Amin Rouy wrote:
Ahan, thanks Justin. Is it default in all versions of Gromacs?
As far as I remember, yes, but don't take my word for it. Look at
mdout.mdp from grompp - it has the full list of every setting that's
being used in your simulation (and also the top of md.log, though some
of those are parsed in ways that make them harder to understand).
-Justin
On Mon, Mar 12, 2018 at 2:44 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 3/12/18 9:31 AM, Mark Abraham wrote:
Hi,
Very many things are often simplified when you make a tutorial. Those .mdp
files are already complicated enough for a beginner.
Indeed, and comm-mode = linear is the default behavior, so it works just
fine without bothering the user to think about such abstract concepts :)
-Justin
Mark
On Mon, Mar 12, 2018 at 2:26 PM Amin Rouy <aminrou1...@gmail.com> wrote:
But, why in some Gromacs tutorial there is no comm-mode used in .mdp file,
for example in 'Lysozyme in water';
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx
-tutorials/lysozyme/index.html
On Mon, Mar 12, 2018 at 1:50 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:
Hi,
If you get this wrong, the equipartition of energy is usually broken and
the simulation is probably unphysical.
Mark
On Mon, Mar 12, 2018, 13:47 Amin Rouy <aminrou1...@gmail.com> wrote:
Dear Justin,
If we do not use comm-mode, which quantity might be changed after
simulations?
Can we remove center of mass after the simulation done?
On Sat, Mar 10, 2018 at 6:36 PM, Amin Rouy <aminrou1...@gmail.com>
wrote:
thank you so much.
On Sat, Mar 10, 2018 at 6:33 PM, Justin Lemkul <jalem...@vt.edu>
wrote:
On 3/10/18 12:31 PM, Amin Rouy wrote:
Thank you Justin.
What if we do not know the phase of the final result? of if we are
in 2
phase region (gas-liquid)
If you're applying PBC you have to use linear as your comm-mode
(grompp
will fail otherwise, so that's a pretty good hint).
-Justin
On Sat, Mar 10, 2018 at 6:25 PM, Justin Lemkul <jalem...@vt.edu>
wrote:
On 3/10/18 12:17 PM, Amin Rouy wrote:
Dear Gromacs people,
I have a question please.
In which condition we must use center of mass removal? Is that
optional or
necessary?
Typically necessary.
and how to know which mode (linear or angular) is better for our
simulations?
Linear is only for condensed-phase systems, angular is only for
vacuum
simulations.
-Justin
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Virginia Tech Department of Biochemistry
303 Engel Hall
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Blacksburg, VA 24061
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Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
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