Dear Amber guys
I am doing simulations on a small (35 amino acids) peptide in an implicit
solvent environment. I find that langevin temperature (using gamma_ln = 1)
control results in a great deal of translational movement and rather little
intra-molecular movement. Indeed, the dynamics of the regions that should be
mobile appear to be quite "stiff". Dynamics with a Berendson thermostat
appears to better reproduce the conformational behaviour of the 20 NMR
structures.
My questions are these:
1. Is there a minimum system size limit that you recommend for langevin
dynamics? I.e. does langevin temperature control cease to work effectively
when the system size is small?
2. Is there a problem with my random number generator? If the collisions are
indeed random then surely the net force over a long simulation period should
approach 0? I.e. It seems suspicious that collisions don't balance out the
translation of the molecule more.
Many thanks
hayden
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Dec 03 2006 - 06:07:14 PST
