can someone comment?

Date: Fri Apr 06 2007 - 22:17:32 CDT

Hi all,
     I have read suggestions at several places in mailing archive about minimizing the system till Gradient Tolerance reaches in single digits or below 1.0 etc. Further, we all know that energy minization is done to remove any bad VDW contacts which may lead to high forces during MD.
 Using the gradient tolerance criterion, i subjected my system to 1000 steps of steepest descents and plotting Total and VDW energy shows a continued decrease in total energy which is ofcourse desired but an increase in VDW energy after an initial decrease. Is it wise to leave the system at high VDW energy even though gradient tolerance is nearly to ~4.0. Any comments on this are highly appreciated.
 Further, Should we keep the essential ions such as "ZN" or other found in most proteins fixed because minimization distorts the ligand geometry most of the time--atleast in my case?

Harish Vashisth (Ph.D Candidate)
CAT-361,Chemical & Biological Engg.
Drexel University, Philadelphia, PA
office: 215-895-5823

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:46:10 CST