On 1/17/18 12:06 PM, Rose wrote:
Thank you so much,I've got it now.
we know that for example 2 molecule can not stick to each other they just close
enough till repulse each other.
Now, imagine pulling, if I can not see "really broken" structures in classicalMD , so
what would be my criterion and clue to say that:"that's enough, you shouldn't pull it
MORE?"
Totally, how can i know the Max pulling ?
I have PMF schemes which show repulsion( after interaction distance the
potential get less minus and tend to get more positive but they just stop in
0kJ and not any positive potential. It happened for every AA which i pull it
through sheet, so i doubt to my results.
A PMF of zero means the biased groups are (effectively) no longer
interacting. You should expect this.
This thread is well off topic of the original post; if you have further
questions, start a new thread to avoid hijacking this one and
complicating the archive further.
-Justin
Sorry for poor english
With regards
Sent from my iPhone
On Jan 17, 2018, at 19:57, Justin Lemkul <jalem...@vt.edu> wrote:
On 1/17/18 11:23 AM, Rose wrote:
I mean, sometimes structures may really break or collapse, in these situations
trjconv won't show these broken structures whole yes?
just will show them broken (as they really are) yes?
In the context of the question I was answering, "broken" means that it appears bonds have broken
and molecules appear at either side of a periodic boundary. That instance is always fixed by proper use of
trjconv. Bonds can't break or form during classical MD, so if trjconv leaves "broken" molecules
behind, then you've got a topology issue. But I'd wager that about 99.999% of the cases that involve
"broken" molecules are normal PBC issues and nothing more.
But, to answer your question, no, trjconv won't fix a situation in which the
user has supplied an incorrect topology.
-Justin
Sent from my iPhone
On Jan 17, 2018, at 18:15, Justin Lemkul <jalem...@vt.edu> wrote:
On 1/17/18 9:40 AM, Rose wrote:
You mean if -pbc could make molecule whole,everything is ok, but if not it
means the molecule was broken from first, yes?
mdrun writes "broken" coordinates because the physics does not depend on our
visualization convenience. Most programs account for PBC. Some don't. It is generally a
safe practice to just make molecules whole as your first step in trjconv and avoid any
ambiguity.
-Justin
Sent from my iPhone
On Jan 17, 2018, at 16:19, Justin Lemkul <jalem...@vt.edu> wrote:
On 1/17/18 5:51 AM, Vidya R wrote:
Hi Justin,
I got the same result as you said.
What confused me was, when I viewed movie.pdb file generated by the
following command,
gmx trjconv -pbc nojump -s PRD-SMP3.gro -f PRD-SMP3.xtc -e 10000.0 -n
index.ndx -o movie.pdb
two hydrogen molecules of my organic compound, were unbonded to my molecule
(which is not supposed to be). They are far away from molecules (their
bonds were broken)
Is it a pbc problem?
Because, when I used
gmx trjconv -pbc whole -s PRD.tpr -f PRD.xtc -o trajwhole.xtc
gmx trjconv -pbc nojump -s PRD.tpr -f trajwhole.xtc -o trajcluster.xtc
gmx trjconv -pbc mol -center -s PRD.tpr -f trajcluster.xtc -o newtraj.xtc
and created a .pdb file with newtraj.xtc, the whole molecule was intact.
Making molecules whole should always be the first step. If you try to remove jumps with
"broken" molecules, what you visualize will be garbage. A separate issue is
with respect to the analysis programs - many are PBC-aware and can handle the original
trajectory without manipulation.
-Justin
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jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
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Justin A. Lemkul, Ph.D.
Assistant Professor
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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Justin A. Lemkul, Ph.D.
Assistant Professor
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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