Dear AMBER users,
When I finished a MD simulation, I want to perform energy minimization on
some structures in MD trajectory, now I have two methods to do that.
1. extract desired frames from trajectory and save the frames as *rst*
files, set *imin=1* in control file
2. extract desired frames from trajectory and save the frames as *crd*
files, set *imin=5* in control file, use -c and -y flags for sander
Other parameters are same for both methods
for imin=5, the following important note is presented in amber manual:
**IMPORTANT CAVEAT: The input coordinate file used (-c <inpcrd>)
should be the same as the input coordinate file used to generate the
original trajectory.
**This is because *sander sets up parameters for PME from the box
coordinates in the input coordinate file*.
My questions are:
1. What does it mean "*sander sets up parameters for PME from the box
coordinates in the input coordinate file*"? What if I chose a different
<inpcrd> for -c flag(i.g., md rst file)
rather than the original <inpcrd> file generated by Leap?
2. I have tried two methods mentioned above and finds that the first
method with "*rst file,imin=1*" gives a lower final enery than the second
method with "*crd file, imin=5*".
Could someone tell me what's the difference between imin=1 and imin=5
when performing minimizations on structures from MD trajectory
Many thanks!
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Aug 01 2014 - 01:30:03 PDT
