which amber version, and have you applied all of the patches?
we have no such trouble with langevin dynamics and implicit solvent.
Hayden Eastwood wrote:
>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
>
>
-----------------------------------------------------------------------
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
