On Tue, May 24, 2011, Jodi Ann Hadden wrote:
> I have come across an interesting problem with SHAKE in TI in Amber
I don't see enough information to really help, but note that you must be very
careful that exactly the same bonds are being shaken (and to the same bond
length) in both V0 and V1. Generally, it is safest to avoid using shake for
any atoms that are being changed in the TI. You can use the "noshakemask"
variable to set this. So, see if looking at your shake list is violating
this rule. (I think the code is supposed to check for this, but the checks
may not be thorough enough.
....dac
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Wed May 25 2011 - 07:30:05 PDT
