On Mon, May 9, 2011 at 1:39 AM, Mark Abraham <[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]> 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 [email protected] > 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 [email protected]. > 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: [email protected] =====================================================
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