Fred, You might want to review the literature on using MD to study diffusion of O2/CO in myoglobin.
Jack John J. Tanner Professor of Biochemistry and Chemistry Associate Chair of Biochemistry Department of Biochemistry University of Missouri 117 Schweitzer Hall 503 S College Avenue Columbia, MO 65211 Phone: 573-884-1280 Email: tanne...@missouri.edu<mailto:tanne...@missouri.edu> http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html Lab: Schlundt Annex rooms 3,6,9, 203B, 203C Office: Schlundt Annex 203A On Jan 23, 2020, at 3:43 AM, Fred Vellieux <frederic.velli...@lf1.cuni.cz<mailto:frederic.velli...@lf1.cuni.cz>> wrote: Dear all, I need to run MD calculations in order to follow the trajectories of a very small molecule inside a protein. From previous calculations (not MD) I have starting positions for this small molecule that all seem in agreement with a possible path of motion inside the protein. Now I need to access a MD program (without licensing costs). I've had a look at the software list provided in Wikipedia (and tried to install the software, in succession, alas without success): cp2k - present for CentOS6 (with yum install ?) but appears to have vanished for CentOS7; gromacs requires a gcc version I don't have (even after having compiled and installed a suitable gcc version, cmake complains about the "old version" and stops); NWChem is unhappy with the Python setup and doesn't compile. I don't know how to solve all these OS version, library, unsuitable binary etc problems. In fact I don't know if any of these 3 software suites would be suitable for what I have in mind. Hence would anyone know of a useful MD software suite that would be suitable for my purpose and comes with statically linked binaries suitable for Intel 64 (Linux) ? Just launch the executable and it runs, no questions asked... Thank you, Fred. ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
