On 10/05/2011 12:24 AM, Dimitar Pachov wrote:
On Mon, May 9, 2011 at 1:39 AM, Mark Abraham <[email protected] <mailto:[email protected]>> wrote:On 9/05/2011 2:01 PM, Dimitar Pachov wrote:Hi, On Sat, May 7, 2011 at 9:45 PM, Justin A. Lemkul <[email protected] <mailto:[email protected]>> 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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