Dimitar Pachov wrote:
On Sat, May 7, 2011 at 11:02 AM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
Dimitar Pachov wrote:
Hello,
I have performed simulations of protein+ligands (solute) in
truncated octahedral unit cell of waters (solvent). I would like
to retain the shape of unit cell and have the solute centered in
such a way as to be completely surrounded by solvent. At this
point, I cannot achieve this although I have exhausted my
knowledge about using the trjconv options. My question is:
1. How can one recenter solvent around solute and at the same
time keep the original unit shape?
I used the following command to get this picture:
trjconv -f run.xtc -s run.tpr -n index-all.ndx -o
traj/run-test.xtc -pbc mol -center -ur compact
Use -ur tric instead of -ur compact.
This does not work. Neither is the solute always surrounded by solvent
for every frame (it goes out of the box) nor is the original unit cell
(truncated octahedron) preserved.
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."
I don't understand how one can achieve this, and if there is a way to do
it, why it has not been clearly explained elsewhere.
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.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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