[gmx-users] Trajectories

[rankinb]

I am interested in pulling out the trajectories (x,y,z coordinates) of water
molecules within a certain distance of my solute molecule.  I have tried
using g_select, but that will only give me the atom numbers and not the
trajectories.  I can create an index file using this command but
unfortunately each time frame is set as a different group.  

Is there a way to get the trajectories at all frames of only the water
molecules within a specified distance of a solute molecule? 

Thank you very much,
Blake

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[gmx-users] XYZ Cordinates of a subsset of atoms

[rankinb]

Is there a way to create a .gro file with the XYZ coordinates of atoms that
are within a specified distance of another atom at each time frame?  It
seems that trjconv should be able to do this but I am having a difficult
time figuring it out. 

Thank you,
Blake



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[gmx-users] trjconv for pbc

[rankinb]

Hi all,

I am trying to use trjconv to remove PBC.  More specifically, I would like
to extract the coordinates of all the water molecules within a certain
distance of a single solute molecule.  However, I have been unsuccessful in
doing so, even after following the guidelines on the GROMACS website
(http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions).
  

Here are some of the things I have tried. First, I extracted the indices of
the water molecules of interest using g_select and used trjconv to extract
the coordinates from the .gro file.  Then I used trjconv -pbc mol on the
resulting .gro file.  The problem is that some of the water molecules are on
opposite sides of the box.

Does anyone have any suggestions?

Thank you very much,
Blake

PhD Candidate 
Purdue University
Ben-Amotz Lab

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[gmx-users] Re: trjconv for pbc

[rankinb]

Tsjerk,

Thanks for your reply.  I have tried using the center option, but ran into
similar problems.  Here are the exact commands that I used:

g_select -f file.xtc -s file.tpr -n index.ndx -select 'group 14 and within
0.71 of group 13' -b 37.875 -e 37.875 -on index1 (where group 14 contains
the water molecules and group 13 is the solute molecule)

trjconv -s file.tpr -n index1.ndx -f file.xtc -o out.gro -b 37.875 -e 37.875

trjconv -f out.gro -s file.tpr -n index.ndx -o out2.gro -center

Does this procedure seem reasonable?

Thanks,
Blake

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[gmx-users] Re: trjconv for pbc

[rankinb]

Here is a snapshot of what I was able to extract, if that helps.

 

Blake

PhD candidate
Purdue University
Ben-Amotz Lab

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[gmx-users] Re: trjconv for pbc

[rankinb]

Here are the steps that I used:

1.  trjconv -pbc whole -dump 37.875
2.  trjconv -pbc nojump
3.  trjconv -center
4.  g_select to make an index containing the atoms of interest
5.  trjconv to extract coordinates

Regardless of whether step 1 is used or not, the resulting coordination
shell configuration is not complete in the sense that it looks like the
figure I posted previously.  In all steps, I used the same .tpr file...is it
possible that I need to generate a new one after step 1?

Thanks,
Blake

PhD candidate
Purdue University
Ben-Amotz Lab

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[gmx-users] Re: trjconv for pbc

[rankinb]

That last procedure works.  I really appreciate your help.  The only other
question I have is related to the selection process.  Is there a way to
select the oxygen atoms of water within a certain distance of a molecule, as
well as the corresponding hydrogen atoms on the water molecule?  Right now,
I am able to select hydrogen atoms and oxygen atoms that are within a
certain distance, but I would like to only select whole water molecules
whose oxygen atoms are within a cutoff.

Thanks,
Blake

PhD Candidate
Purdue University
Ben-Amotz Lab

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[gmx-users] Number of water molecules around any methyl carbon

[rankinb]

Hi all,

I would  like to calculate the number of water molecules around any of the
methyl carbon atoms of tert-butyl alcohol.  Currently, I have defined an
index group containing all three of the methyl carbon atoms and used
trjorder -nshell to calculate the number of oxygen atoms within a specified
cutoff distance of this index group.  What I am trying to figure out is
whether this method results in the number of oxygen atoms around any single
methyl carbon or all methyl carbon atoms.  Does anyone have any insights
regarding this problem?  If the described method does not calculate the
number of oxygen atoms around all of the methyl carbon atoms, is there a way
to do so, without overcounting?  

Thanks,
Blake

PhD Candidate
Purdue University
Ben-Amotz Lab

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