[gmx-users] How to recenter solvent around solute

[Mark Abraham]

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?

Mark
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