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 criterio
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
enoug
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
a
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?
Sent from my iPhone
> On Jan 17, 2018, at 18:15, Justin Lemkul wrote:
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>> On 1/17/18 9:40 AM, Rose wr
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. So
You mean if -pbc could make molecule whole,everything is ok, but if not it
means the molecule was broken from first, yes?
Sent from my iPhone
> On Jan 17, 2018, at 16:19, Justin Lemkul wrote:
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>> On 1/17/18 5:51 AM, Vidya R wrote:
>> Hi Justin,
>>
>> I got the same result as you said.
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 1.0 -n
index.ndx -o movie.pdb
two hydrogen molecules of
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 1.0 -n
index.ndx -o movie.pdb
two hydrogen molecules of my organic compound, were unbonded to my
On 1/13/18 7:53 AM, Vidya R wrote:
Hi gmx users,
I used the following commands after simulation run (organic compound in
water, to calculate rdf)
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 trjc
Hi gmx users,
I used the following commands after simulation run (organic compound in
water, to calculate rdf)
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 trajcl
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