[gmx-users] simulation with amber10 and gromacs 4.5.1

Justin A. Lemkul jalemkul at vt.edu
Wed Sep 14 15:53:17 CEST 2011

vijayaraj ramadoss wrote:
> Hello Users,
> Previous I have done simulation of small protein using Amber10 with 
> ff99sb force field. I did the same calculation using the gromacs 4.5.1 
> with amber ff99sb force field. I found a loop segment takes much more 
> fluctuation with gromacs simulation and which was not observed with the 
> amber10 simulation. can anyone explain me why this happens.

Did you run replicates of each system, or are you basing your observations on a 
single trajectory?  You need to compare properly sampled systems.  A single 
trajectory is generally not enough to make reliable conclusions.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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