Hi Nilesh,
To center the solute with respect to the solvent, first center the
solute in the box, and then put the solvent in the box. Mind that that
involves two passes of trjconv.
If 'no pbc effect' means no wrapping over the boundaries, yes you can
use -dump with -pbc nojump to save a snapshot.
Ya, I want to center solute w.r.t to the solvent.
I have more question, if I want to save the coordinates of a snapshot with
no pbc effect, can I use -pbc nojump in trjconv.
nilesh
On Mon, October 17, 2011 1:34 pm, Tsjerk Wassenaar wrote:
> Hey :)
>
>
> The reference plays no role in centering.
Hey :)
The reference plays no role in centering. But I guess that Nilesh expects
centering of the solute w.r.t. to the solvent, or is looking at the wrong
center (tric/rect).
Cheers,
Tsjerk
On Oct 17, 2011 7:06 PM, "Justin A. Lemkul" wrote:
Nilesh Dhumal wrote: > > Thanks Justin, > > Still so
Nilesh Dhumal wrote:
Thanks Justin,
Still solute is not at center.
Is your reference frame (i.e. the .tpr file) centered? If not, centering likely
won't work as desired. I assumed that it was centered, per normal system
building procedures.
-Justin
Nilesh
On Mon, October 17, 2011
Thanks Justin,
Still solute is not at center.
Nilesh
On Mon, October 17, 2011 11:27 am, Justin A. Lemkul wrote:
>
>
> Nilesh Dhumal wrote:
>
>> In 2nd step I choose system instaed of solvent.
>>
>>
>> I could not make the solute at the center.
>>
>>
>
> Don't use -b and -e when running trjconv
Nilesh Dhumal wrote:
In 2nd step I choose system instaed of solvent.
I could not make the solute at the center.
Don't use -b and -e when running trjconv. I have found that PBC routines are
not always correctly applied when parsing out sections of the trajectory. This
can affect your ab
In 2nd step I choose system instaed of solvent.
I could not make the solute at the center.
Thanks
NIlesh
On Mon, October 17, 2011 11:05 am, Justin A. Lemkul wrote:
>
>
> Nilesh Dhumal wrote:
>
>> Justin,
>>
>>
>> I have 26 solute atoms and 3302 solvent atoms in my sytems (total 3328
>> atoms).
Nilesh Dhumal wrote:
Justin,
I have 26 solute atoms and 3302 solvent atoms in my sytems (total 3328
atoms).
1. trjconv -f 3.trr -s 3.tpr -pbc mol -b 400 -e 600 -dt 1 -n 500-1.ndx -o
4-600.xtc
here I choose group 0:system (3328 atoms)
2. trjconv -f 4-600.xtc -s 3.tpr -n 500-1.ndx -center
Justin,
I have 26 solute atoms and 3302 solvent atoms in my sytems (total 3328
atoms).
1. trjconv -f 3.trr -s 3.tpr -pbc mol -b 400 -e 600 -dt 1 -n 500-1.ndx -o
4-600.xtc
here I choose group 0:system (3328 atoms)
2. trjconv -f 4-600.xtc -s 3.tpr -n 500-1.ndx -center -o 4-600-1.xtc
For Cent
Nilesh Dhumal wrote:
Hello,
I have system with solute is surrounded by 256 solvent molecules. I run
the simulation for 20 ns. I save the snap shot at 500 ps using following
command.
trjconv -f 3.trr -s 3.tpr -n 500-1.ndx -b 500.0 -e 501.0 -dt 1.0 -pbc
nojump -center -o 500-11.pdb
I tried t
Hello,
I have system with solute is surrounded by 256 solvent molecules. I run
the simulation for 20 ns. I save the snap shot at 500 ps using following
command.
trjconv -f 3.trr -s 3.tpr -n 500-1.ndx -b 500.0 -e 501.0 -dt 1.0 -pbc
nojump -center -o 500-11.pdb
I tried to keep the solute at the
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