Dear Sir/Madam,
I am interested to study a reaction coordinate as follows:
X + C-Y ==> X-C-Y ==> X-C + Y
It seems to me that I should define the reaction coordinate as the distances of XtoC and CtoY.
The LCOD patch used in tutorial A10 seems to serve this purpose for Steered MD calculation.
However, if I am doing PMF with umbrella sampling, can I should use the LCOD commands?
Best regards,
Cat
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Aug 06 2010 - 01:00:02 PDT
