Asmaa Elsheshiny wrote:
Hi, I am simulating a protein in water. But I have forgotten to center the
protein from the beginning to the origin. So, is it possible to center the
When using periodic boundary conditions, the "center" of the system is an
arbitrary designation. Gromacs builds boxes from the origin, so even if you had
centered the protein, it wouldn't have been at the origin.
protein to the origin in the trajectory file? And if it is not possible, how
trjconv -boxcenter zero, if you really think you need to do this.
-Justin
can obtain the atomic positions independent of the center of mass, to use
for further analysis? Cheers, Asmaa
--
========================================
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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