Nilesh Dhumal wrote:
Hello Justin,
THanks for your reply.
Suppose any atom that leaves a simulation box by, say, the right-hand
face, then enters the simulation box by the left-hand face.
For these atom how gromacs save the coordinate.
Does it save the coordinate when it enter from left-hand face?
Presumably. Look in the code, but I suspect this is indeed the case and the
reason why trjconv -pbc nojump and other such operations are useful.
-Justin
Nilesh
On Wed, April 13, 2011 9:26 pm, Justin A. Lemkul wrote:
Nilesh Dhumal wrote:
Hello,
If some part of molecule is outside the box. How Gromacs save the
coordinates in trajectory.
There is no such thing as "outside" in a periodic system.
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Condit
ions
-Justin
Nilesh
--
========================================
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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========================================
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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