[gmx-users] essential dynamics and flooding

Oskar Berntsson oskar.berntsson at gu.se
Mon Aug 3 11:27:59 CEST 2015

Dear all,

I am simulating a protein and I want to sample conformations that are not commonly sampled using an equilibrium simulation. As far as I figure, what I want to use is essential dynamics.

I am using gromacs VERSION 4.5.5

My protein consists of ca 600 residues.

I have run a 250 ns equilibrium simulation and calculated eigenvectors for the ca 600 Calphas using g_covar.

I have tested to run essential dynamics using radial acceptence sampling and flooding, but I cannot seem to get it to work as I intend.

I have studied the manual and the referenced literature but I cannot find out why I cannot get it to work.

1) When I use radial acceptence sampling the protein rapidly "unfolds". I have tried the commands below to generate my .edi file, in this case with the specific intention to make the protein not unfold.

I would expect the simulation to run "maxedsteps" before a new expansion but after the first "eqsteps" the acceptance radius just increases with every step, which quickly deforms the protein and the simulation aborts after ca 2*maxedsteps steps.

> make_edi -s struct.gro -f eigenvec.trr -eig eigenval.xvg -n index.ndx -radacc 1-3 -slope -1 -maxedsteps 500000 -eqsteps 500000 -mon 1-3 -o sam.edi

> make_edi -s struct.gro -f eigenvec.trr -eig eigenval.xvg -n index.ndx -radacc 1-3 -slope 0 -maxedsteps 500000 -eqsteps 500000 -mon 1-3 -o sam.edi

2) When I have used flooding I rather have the opposite problem. I cannot force the structure to change one bit over a 50 ns simulation. I have attempted both constant flooding and adaptive flooding.

Typically I have generated .edi files as follows

> make_edi -s struct.gro -f eigenvec.trr -eig eigenval.xvg -n index.ndx -flood 1-3 -alpha 2 -o sam.edi -deltaF0 5 -tau 200

> make_edi -s struict.gro -f eigenvec.trr -eig eigenval.xvg -n index.ndx -flood 1-3 -tau 0 -Eflnull 10 -alpha 2 -o sam.edi

and I have used different deltaF0, tau and Eflnull

-deltaF0 = 5-50000000 kJ/mol, tau = 200ps -20 ns and -Eflnull 10-500000000 kJ/mol

Any help would be greatly appreciated.

Best regards


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