From: dbaogen (dbaogen_at_gmail.com)
Date: Fri Nov 15 2013 - 02:42:07 CST
In the course of using SMD method, I am confused about whether I can use SMD and TclForces keywords simultaneously? Such as, in the NAMD configuration file, the following parameters are set for pulling one ligand out from protein:
SMDk 1.2 ;#unit kcal/mol/angstrom
SMDVel 0.00002 ;#angstrom/timestep
SMDDir 0.602154 -0.325362 -0.729075
SMD keyword is set for pulling ligand. And Tclforces keyword is set to avoid protein rotation and transition in SMD simulation
Using the above parameters in the configuration file, I have some puzzles about simulation result.
(1) The dummy atom which is attached to the ligand (SMD atoms) moves 3 angstrom, but the COM of SMD atoms is moved 8 angstrom which is larger than the drift distance of dummy atom.
(2) If we continue to run SMD simulation after the ligand is pulled out from the active site of protein, the system is unstable and collapsed.
Now, I could not find the solution of these problems. Would you like to give me some help? Thanks in advance !
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