Re: [gmx-users] trjconv:solute at the center

2011-10-17 Thread Tsjerk Wassenaar
Hi Nilesh, To center the solute with respect to the solvent, first center the solute in the box, and then put the solvent in the box. Mind that that involves two passes of trjconv. If 'no pbc effect' means no wrapping over the boundaries, yes you can use -dump with -pbc nojump to save a snapshot.

Re: [gmx-users] trjconv:solute at the center

2011-10-17 Thread Nilesh Dhumal
Ya, I want to center solute w.r.t to the solvent. I have more question, if I want to save the coordinates of a snapshot with no pbc effect, can I use -pbc nojump in trjconv. nilesh On Mon, October 17, 2011 1:34 pm, Tsjerk Wassenaar wrote: > Hey :) > > > The reference plays no role in centering.

Re: [gmx-users] trjconv:solute at the center

2011-10-17 Thread Tsjerk Wassenaar
Hey :) The reference plays no role in centering. But I guess that Nilesh expects centering of the solute w.r.t. to the solvent, or is looking at the wrong center (tric/rect). Cheers, Tsjerk On Oct 17, 2011 7:06 PM, "Justin A. Lemkul" wrote: Nilesh Dhumal wrote: > > Thanks Justin, > > Still so

Re: [gmx-users] trjconv:solute at the center

2011-10-17 Thread Justin A. Lemkul
Nilesh Dhumal wrote: Thanks Justin, Still solute is not at center. Is your reference frame (i.e. the .tpr file) centered? If not, centering likely won't work as desired. I assumed that it was centered, per normal system building procedures. -Justin Nilesh On Mon, October 17, 2011

Re: [gmx-users] trjconv:solute at the center

2011-10-17 Thread Nilesh Dhumal
Thanks Justin, Still solute is not at center. Nilesh On Mon, October 17, 2011 11:27 am, Justin A. Lemkul wrote: > > > Nilesh Dhumal wrote: > >> In 2nd step I choose system instaed of solvent. >> >> >> I could not make the solute at the center. >> >> > > Don't use -b and -e when running trjconv

Re: [gmx-users] trjconv:solute at the center

2011-10-17 Thread Justin A. Lemkul
Nilesh Dhumal wrote: In 2nd step I choose system instaed of solvent. I could not make the solute at the center. Don't use -b and -e when running trjconv. I have found that PBC routines are not always correctly applied when parsing out sections of the trajectory. This can affect your ab

Re: [gmx-users] trjconv:solute at the center

2011-10-17 Thread Nilesh Dhumal
In 2nd step I choose system instaed of solvent. I could not make the solute at the center. Thanks NIlesh On Mon, October 17, 2011 11:05 am, Justin A. Lemkul wrote: > > > Nilesh Dhumal wrote: > >> Justin, >> >> >> I have 26 solute atoms and 3302 solvent atoms in my sytems (total 3328 >> atoms).

Re: [gmx-users] trjconv:solute at the center

2011-10-17 Thread Justin A. Lemkul
Nilesh Dhumal wrote: Justin, I have 26 solute atoms and 3302 solvent atoms in my sytems (total 3328 atoms). 1. trjconv -f 3.trr -s 3.tpr -pbc mol -b 400 -e 600 -dt 1 -n 500-1.ndx -o 4-600.xtc here I choose group 0:system (3328 atoms) 2. trjconv -f 4-600.xtc -s 3.tpr -n 500-1.ndx -center

Re: [gmx-users] trjconv:solute at the center

2011-10-17 Thread Nilesh Dhumal
Justin, I have 26 solute atoms and 3302 solvent atoms in my sytems (total 3328 atoms). 1. trjconv -f 3.trr -s 3.tpr -pbc mol -b 400 -e 600 -dt 1 -n 500-1.ndx -o 4-600.xtc here I choose group 0:system (3328 atoms) 2. trjconv -f 4-600.xtc -s 3.tpr -n 500-1.ndx -center -o 4-600-1.xtc For Cent

Re: [gmx-users] trjconv:solute at the center

2011-10-17 Thread Justin A. Lemkul
Nilesh Dhumal wrote: Hello, I have system with solute is surrounded by 256 solvent molecules. I run the simulation for 20 ns. I save the snap shot at 500 ps using following command. trjconv -f 3.trr -s 3.tpr -n 500-1.ndx -b 500.0 -e 501.0 -dt 1.0 -pbc nojump -center -o 500-11.pdb I tried t

[gmx-users] trjconv:solute at the center

2011-10-16 Thread Nilesh Dhumal
Hello, I have system with solute is surrounded by 256 solvent molecules. I run the simulation for 20 ns. I save the snap shot at 500 ps using following command. trjconv -f 3.trr -s 3.tpr -n 500-1.ndx -b 500.0 -e 501.0 -dt 1.0 -pbc nojump -center -o 500-11.pdb I tried to keep the solute at the