[gmx-users] How to recenter solvent around solute

[Mark Abraham]

On 10/05/2011 12:24 AM, Dimitar Pachov wrote:
>
>
> On Mon, May 9, 2011 at 1:39 AM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>
>     On 9/05/2011 2:01 PM, Dimitar Pachov wrote:
>>     Hi,
>>
>>     On Sat, May 7, 2011 at 9:45 PM, Justin A. Lemkul <jalemkul at vt.edu
>>     <mailto:jalemkul at vt.edu>> wrote:
>>
>>
>>         Please clarify - do you wish to maintain the original
>>         triclinic representation (as -ur tric does) or do you wish to
>>         see the octahedral representation (as -pbc mol -ur compact
>>         gives)?  My answer was based on your request to "keep the
>>         original unit shape."
>>
>>
>>     My original representation is truncated octahedron. Gromacs
>>     requires triclinic vectors and does not care about unit cell
>>     shape at the moment the md code starts. I wanted to keep MY
>>     original unit shape.
>>
>>
>>
>>         For complicated systems (or sometimes even for simple ones),
>>         it is quite common that multiple iterations of trjconv are
>>         necessary.  A suggested workflow is indeed documented:
>>
>>         http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow
>>
>>         The documentation must remain somewhat generic, as there are
>>         a number of specialty systems that can be considered.
>>
>>
>>     I thought the guidelines given by the trjconv specific manual
>>     were sufficient. I don't understand why people don't put this
>>     suggested workflow in the trjconv manual. It is confusing
>>     otherwise. It never came to me that one needed multiple usages of
>>     trjconv in order to achieve recentering around solute.
>
>     Fair point. I've updated the trjconv documentation to provide this
>     hint and a suggestiong to consult the webpage.
>
>
>>     I followed these instructions and got what I wanted. Basically,
>>     this was my quick workflow:
>>
>>     =================================
>>     psfinname="$prot-$shape-$flc"
>>     topfile="$prot-$shape-$flc.top"
>>     grofile="$shape-$fl-eq.gro"
>>     inpfile="md.mdp"
>>
>>     name="run1"
>>     newname="run1-recen"
>>     indexfile="index-all.ndx"
>>     tclfile="extr-frame-traj.tcl"
>>
>>     s="Protein-Nucleo"
>>     indsolute=`cat $indexfile | awk -v site=$s
>>     '$1=="["{i++}$2==site{print i-1}'`
>>     cp $name.xtc $newname.xtc
>>
>>     #===> 1
>>     intraj="$newname.xtc"
>>     outtraj="traj/$newname-whole.xtc"
>>     trjconv -f $intraj -s $name.tpr -n $indexfile -o $outtraj  -pbc
>>     whole > log1 2>&1 <<EOF1
>>     0
>>     EOF1
>>     #===> 2
>>     intraj="$outtraj"
>>     outtraj="traj/$newname-cluster.xtc"
>>     trjconv -f $intraj -s $name.tpr -n $indexfile -o $outtraj  -pbc
>>     cluster > log2 2>&1 <<EOF2
>>     $indsolute
>>     0
>>     EOF2
>>     #===> 3
>>     intraj="$outtraj"
>>     outtraj="traj/$newname-nojump.xtc"
>>     trjconv -f $intraj -n $indexfile -o $outtraj  -pbc nojump > log3
>>     2>&1 <<EOF3
>>     0
>>     EOF3
>>     #===> 4
>>     intraj="$outtraj"
>>     outtraj="traj/$newname-center.xtc"
>>     trjconv -f $intraj -n $indexfile -o $outtraj  -center > log4 2>&1
>>     <<EOF4
>>     $indsolute
>>     0
>>     EOF4
>>     #===> 5
>>     ## Get first frame from centered .xtc
>>     fr=1
>>     pdbfilename="`echo $outtraj | awk 'BEGIN{FS="."}{print $1}'`"
>>     pdbfile="$pdbfilename-${fr}ps.pdb"
>>     `which vmd` -dispdev text -e $tclfile -args $fr
>>     ${pathpsfin}/${psfinname}.psf $outtraj $pdbfilename > /dev/null
>>
>>     cat $pdbfile | sed 's/TIP3/SOL /' | sed 's/ OH2 SOL/ OW  SOL/' |
>>     sed 's/ H1  SOL/ HW1 SOL/' | sed 's/ H2  SOL/ HW2 SOL/' | sed 's/
>>     SOD SOD/ NA  NA /g' | sed 's/ CLA CLA/ CL  CL /g' | sed 's/ HT1
>>     MET/ H1  MET/' | sed 's/ HT2 MET/ H2  MET/' | sed 's/ HT3 MET/ H3
>>      MET/' > $pdbfilename-${fr}ps-renamed.pdb
>>
>>     grompp -f $inpfile -c $pdbfilename-${fr}ps-renamed.pdb -n
>>     $indexfile -p $topfile -o $newname-center.tpr > log5 2>&1
>>     #===> 6
>>     intraj="$outtraj"
>>     outtraj="traj/$newname-compact.xtc"
>>     trjconv -s $newname-center.tpr -f $intraj -n $indexfile -o
>>     $outtraj  -pbc mol -ur compact > log6 2>&1 <<EOF6
>>     0
>>     EOF6
>>     =================================
>>
>>
>>     However, it seems a long process, and if I have a large number of
>>     trajectories, it might not be feasible. I actually do not know if
>>     all steps are necessary. Particularly, I did step #5 just to get
>>     a new *tpr file from the centered trajectory ... Is there a way
>>     to do that in a simpler way within Gromacs?
>
>     What steps are necessary depends what your purpose is. trjconv
>     -dump should do step #5. What are you generating the centered
>     trajectory for? What are you generating another .tpr for?
>
>
> Since I am new to Gromacs, there are certain things I do not quite 
> understand. I do step #5 only because I need a *tpr file corresponding 
> to the centered trajectory, which I need for step #6, i.e. to finally 
> make the trajectory compact. As far as I understood, I couldn't use 
> the very original *tpr file for the last step #6, correct?

The final call to trjconv uses the .tpr only to learn the definitions of 
molecules, so I think the original one will do. That omits #5 altogether.

> And I need the centered trajectory in order to move to my final goal, 
> i.e. the compact the trajectory at step #6. Again, I thought that the 
> "centering" step was necessary after the "nojump" trajectory had been 
> obtained...

I dunno - try with and without if you want to simplify.

> Also, can one use the trjconv -dump without a *tpr file? I do not 
> think so.

The -s file (which sometimes doesn't need to be a .tpr file, see trjconv 
-h for list of file types for -s) is just used for atom names and such. 
So anything will do.

> Which *tpr file should I use in order to get the first frame from the 
> centered trajectory, and where (and how) should I get this file from 
> (unless I can use the very original one)?

The coordinates in the .tpr file matter only if they're being used, and 
I think they're not being used in any of your steps.

Mark
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