[gmx-users] "B" state for free energy corrupts minimization?

David Mobley dmobley at gmail.com
Tue Jan 31 17:45:46 CET 2006


I agree with Berk -- I'm doing free energy calculations with the Pande group
AMBER port and get no problems. For electrostatic calculations I generally
get good agreement with what I get in the AMBER simulation package itself
(things are different for the vdW component since AMBER doesn't have soft
core) so it seems to be working properly. So I'd look closely at your
topologies and run input. What have you turned on during the minimization
you're running? Try it with free_energy=no; also, have you tried using soft
core or something? (It seems possible that you might occasionally get
strange things in minimization if you use soft core with odd parameters).
Also, make sure your torsion parameters, etc. are set properly, and check
for warnings. Again, I've never seen anything like this, so I strongly
suspect there's something funny going on on your end.


On 1/31/06, mernst at tricity.wsu.edu <mernst at tricity.wsu.edu> wrote:
> I am attempting to perform a free energy simulation that involves the
> transformation of the lesioned DNA base 8-oxoguanine to guanine. Before I
> set up the B state in my .itp file, I was able to simulate 8-oxoguanine
> with MD and its behavior looked to be in reasonable agreement with
> simulations I have performed in another package.
> Now that I have defined B-state parameters, MD and even energy
> minimization give strange and undesirable results, even before I begin the
> free energy calculations or set lambda to a non-zero value.
> I've narrowed it down to a simple test case where I supply a B state for
> just one atom.
> If I use this line in my .itp file, which changes nothing between A and B,
> the energy minimization gives a reasonable-looking structure:
> 46 amber99_35 2 8oG  N7   46   -0.5129    14.01   amber99_35 -0.5129 14.01
> This is what the output looks like:
> http://www.sciencemadness.org/scipics/goodtrimer.png
> If I use this line, using a different atom type in the B state,
> 46 amber99_35 2 8oG  N7   46   -0.5129    14.01   amber99_36 -0.5129 14.01
> the minimization gives me a hydrogen that sticks out at a strange angle:
> http://www.sciencemadness.org/scipics/badtrimer.png
> The amber99_35 atom is AMBER type NA, corresponding to sp2 N in 5
> memb.ring w/H atom (HIS). The amber99_36 atom is AMBER type NB,
> corresponding to sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA). In the A state
> there is a hydrogen that becomes a dummy in the B state, so I would like
> to go from NA to NB. The AMBER force field port to Gromacs is from the
> Pande group.
> I cannot figure out why this effect shows up when lambda=0, and how I
> might set up the free energy simulation so that it is not horribly
> distorted and prone to crashing in the equilibrium period.
> Matt Ernst
> Washington State University
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