On 3/13/13 1:32 AM, Nidhi Katyal wrote:
Dear all
I would like to know the number of oxygen atoms of my co-solvent
molecules which are around 0.3nm of the protein in the last few ns. I
have read the manual and found that trjorder could serve the purpose.
So i have first created index file
Dear all
I would like to know the number of oxygen atoms of my co-solvent
molecules which are around 0.3nm of the protein in the last few ns. I
have read the manual and found that trjorder could serve the purpose.
So i have first created index file containing all the oxygen atoms of
my co-solvent
Hi,
I am trying to use trjorder command to generate a sorted trajectory where all
the water molecules are certain distance away. I can use the trjorder command
to
generate the sorted trajectory where all waters are sorted based on distance
but
I am looking for method for creating a index
Sanku M wrote:
Hi,
I am trying to use trjorder command to generate a sorted trajectory
where all the water molecules are certain distance away. I can use the
trjorder command to generate the sorted trajectory where all waters are
sorted based on distance but I am looking for method for
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
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
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
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
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
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
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
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
Dear Gromacs Users,
I'm using trjorder with the following options:
$ trjorder -f systemWithSolv.xtc -n system.atom.ndx -s system.pdb -r
0.35 -nshell system0.35.nshell.xvg
As the first group I select all the atoms of a single TYR residue,
which is part of a larger protein. As the second group I
Henri Mone wrote:
Dear Gromacs Users,
I'm using trjorder with the following options:
$ trjorder -f systemWithSolv.xtc -n system.atom.ndx -s system.pdb -r
0.35 -nshell system0.35.nshell.xvg
As the first group I select all the atoms of a single TYR residue,
which is part of a larger protein.
Hi all:
I am trying to know how many and which molecules of solvent are near my
system, I read the manual and I found that one can do this using trjorder,
but I can not do this with my Gromacs version 3.3.2 beacause in this
version there is a problem and one can not use options -o and -r
[EMAIL PROTECTED] wrote:
Hi all:
I am trying to know how many and which molecules of solvent are near my
system, I read the manual and I found that one can do this using trjorder,
but I can not do this with my Gromacs version 3.3.2 beacause in this
version there is a problem and one can not
Dmytro Kovalskyy wrote:
It works fine for me under 3.3.1 - what command line are you issuing?
trjorder -f traj.xtc -s topol.tpr -o 5A -nshell 5A -r 0.5
Thanks, this work for me. However, It is not obvious from the help. An
output trajectory is not defined as Option and i supposed it is written
It works fine for me under 3.3.1 - what command line are you issuing?
trjorder -f traj.xtc -s topol.tpr -o 5A -nshell 5A -r 0.5
-Justin
Quoting Dmytro Kovalskyy [EMAIL PROTECTED]:
Trjorder does not write trajectory file, only nshell.xvg
This is true for 3.3.2 and 3.3.1 versions.
Dima
Use the -na and -da flags. trjorder doesn't know how to order the molecules
without these.
-Justin
Quoting Dmytro Kovalskyy [EMAIL PROTECTED]:
It works fine for me under 3.3.1 - what command line are you issuing?
trjorder -f traj.xtc -s topol.tpr -o 5A -nshell 5A -r 0.5
-Justin
Dmytro Kovalskyy wrote:
It works fine for me under 3.3.1 - what command line are you issuing?
trjorder -f traj.xtc -s topol.tpr -o 5A -nshell 5A -r 0.5
Reading the source, both -nshell and -r enforce no trajectory output.
Mark
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Trjorder does not write trajectory file, only nshell.xvg
This is true for 3.3.2 and 3.3.1 versions.
Dima
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It works fine for me under 3.3.1 - what command line are you issuing?
-Justin
Quoting Dmytro Kovalskyy [EMAIL PROTECTED]:
Trjorder does not write trajectory file, only nshell.xvg
This is true for 3.3.2 and 3.3.1 versions.
Dima
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