TJ Mustard wrote:
First off I am using gromacs 4.5. I will also post all of my files and
errors if they help.
If I run a protein in GROMOS96 all my md runs complete succesfully. But
if I change to any of the AMBER force fields I get LINCS errors in my
positional restraint md run. I have tried using shake, 1 fs step sizes,
-heavyh, and many more. Does anyone know what is going on here?
A complete (but not overly lengthy) post will save everyone a lot of time.
Based on the information you've provided here, I see now way to diagnose the
problem. The most important information to post would be your .mdp file.
Certain settings can influence stability. A description of the hardware,
compilers used, etc. can also be useful.
-Justin
The reason I want to use AMBER is the fact that I want to run md on the
30s rybosome and amber converts RNA much easier than GROMOS force fields.
Thank you in advance,
TJ Mustard Email: musta...@onid.orst.edu
Cell: 509-879-4173
--
========================================
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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