Dear Amber Users,
I was wondering about keywords related to periodic simulations:
NSCM and NDFMIN.
NSCM parameter regularly removes the center of mass motion:
check COM velocity, temp: 0.000048 0.00(Removed)
(and the trajectory is altered due to this), but the manual says:
"This flag is ignored for both belly and periodic
simulations" (although under "Special notes about
the PME" the manual suggests to use NTCM/NSCM options).
Also, I read in a recent JACS article with AMBER,
that: "the center of mass velocity was removed during
the production dynamics periodically at intervals
of 10 ps." (-referring to the flying ice cube problem).
So, if it works well, the COM would limit the translation
of the system (not the rotation) - what vaule of NDFMIN is
appropriate and where is it used at all? It seems to me
that this parameter is not used, it is not even echoed
back in the output under "CONTROL DATA FOR THE RUN"
and does seem to make a difference if it is 0 or 6.
Thanks for comments,
Peter
PS: in an unrelated problem I got an error
when I used group constrain with ntr=1:
5. REFERENCE ATOM COORDINATES
----- READING GROUP 1; TITLE:
heating the system
rfree: Error decoding variable 1 3 from:
&cntrl
and it seems this information needs to be read
from the top of the input file and not from the
bottom - which is a bit bizarre.
Received on Thu Feb 01 2001 - 07:24:55 PST
