- From: Alice NgarKit Ko <ako - at - cse.nd.edu>
- Subject: charmm problems
- Date: Mon, 24 Jun 2002 10:47:44 -0500 (EST)
I have a few questions on running charmm simulations.
1) I have this protein pdb file from protein data bank. It has a -9
charge. Do I need to add 9 Na+ to balance the charge? If yes, how and
where do I add them?
2) After taking care of the charge and solvation, how long do I need to
minimize the system? Or how do I know if the system is minimized?
3) After minimization and heating the system back to 300K, how kind of
output files do I need to anaylsis the dyanmics? Unformatted trj? What
will be the other options of output file?
Thanks in advance for your time and help.