Arthur Roberts wrote:
Hi, all,
I am looking for a way in gromacs or manually to make all the angles,
etc. ideal. Perhaps, there is a way to energy minimize a specific
subset of residues or a single residue. Your advice would be greatly
appreciated.
Couldn't you just specify very strong force constants for all the bonds, angles,
etc? Even in the absence of increased force constants, an in vacuo minimization
should produce pretty good geometry, should it not? Using constraints should
help as well, even perhaps "constraints = all-angles."
To minimize only a subset, you could perhaps freeze the other atoms, but that
can be tricky depending on the rest of the .mdp settings. Perhaps a strong
position restraint on anything you don't want to move? You can use genrestr
with a custom index group to specify the atoms to be restrained.
-Justin
Sincerely,
Art
Dr. Arthur Roberts, Ph.D.
University of California, San Diego
Skaggs School of Pharmacy and Pharmaceutical Sciences
9500 Gilman Drive #0703
La Jolla, CA 92093-0703
email: [email protected] <mailto:[email protected]>
cell: 206-850-7468
office: 858-822-7804
fax: 858-246-0089
--
========================================
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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