[gmx-users] How to recenter solvent around solute

[Dimitar Pachov]

On Mon, May 9, 2011 at 1:39 AM, Mark Abraham <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> 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?

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...

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

Thanks,
Dimitar






> Mark
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
=====================================================
*Dimitar V Pachov*

PhD Physics
Postdoctoral Fellow
HHMI & Biochemistry Department        Phone: (781) 736-2326
Brandeis University, MS 057                Email: dpachov at brandeis.edu
=====================================================
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110509/a67fb553/attachment.html>