shivangi nangia wrote:
Thanks Justin, that was helpful.
I have a following question.
Since in my system I have both methanol and water and I want to order
both of them ( my eventual aim to make a sphere), is there is way to
override -na option ( for water na 4, methanol 3).
Is there is way
Thanks Justin, that was helpful.
I have a following question.
Since in my system I have both methanol and water and I want to order both
of them ( my eventual aim to make a sphere), is there is way to override -na
option ( for water na 4, methanol 3).
Is there is way that all the components of th
shivangi nangia wrote:
Hello,
Came back to the set of calculations I was doing few days back.
I have a box of water (TIP4P), methanol, protein and DHB anions.
I minimized this system.
Trying to use trjorder for water molecules with respect to the protein
(eventually I want to make a sphere
Hello,
Came back to the set of calculations I was doing few days back.
I have a box of water (TIP4P), methanol, protein and DHB anions.
I minimized this system.
Trying to use trjorder for water molecules with respect to the protein
(eventually I want to make a sphere by ordering and getting rid
On 4/29/2011 11:29 AM, shivangi nangia wrote:
Hello,
The manual explaining trjorder says:
trjorder orders molecules according to the smallest distance to atoms
in a reference group or on z-coordinate (with option -z). With
distance ordering, it will ask for a group of reference atoms and a
g
Hello,
The manual explaining trjorder says:
trjorder orders molecules according to the smallest distance to atoms in a
reference group or on z-coordinate (with option -z). With distance ordering,
it will ask for a group of reference atoms and a group of molecules. For
each frame of the trajectory
On 4/29/2011 4:08 AM, shivangi nangia wrote:
Hello all,
I am trying to order the TIP4P water molecules in my system with
respect to the polypeptide in my system.
The command I am using is:
trjorder -f shape.gro -s shape.tpr -da 0 -na 4 -o ordered.gro
This runs without any error and ordere
Hello all,
I am trying to order the TIP4P water molecules in my system with respect to
the polypeptide in my system.
The command I am using is:
trjorder -f shape.gro -s shape.tpr -da 0 -na 4 -o ordered.gro
This runs without any error and ordered.gro is generated with random
sequence of water
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