Halie Shah wrote:
Hi!
I'm am trying to visualize the energy minimization trajectory path of my
protein+ligand in VMD. I imported the .trr file into the ending energy
minimized pdb file, and I was able to see the frames of the trr (53 all
together with nstxout=1). But when I ran the trajectory I saw barely any
change in the position on my protein. It just shifted slightly before
the last frame. The rest of the time, the protein was stationary. My
protein is 243 residues, so not very large, and it includes the ligand
(small as well) and the protein; I have constrained nothing. I'm using
Gromacs 4.0.4.
That's not unexpected. You're only doing EM, there shouldn't be any drastic
changes.
When I did the energy minimization, the em.log output file did say that
the protein converged to machine precision but not to my specified
precision (Fmax<100), and that my stepsize might be too small or the
energy change not significant. Is this message a problem? Is it because
maybe my energy change isn't significant, that my protein is not
fluctuating much? The em.log output file showed that it took 79 steps,
steepest descent, to minimize my protein..the beginning potential was
-1.5E5 kj/mol and the ending potential was -4.9E5....I graphed the
energies vs step and it did show a significant, stable convergence of
potential.
Check the archives for advice; this question is asked often. Generally Fmax <
1000 is adequate for a simple protein system, so 100 is often too rigorous.
Anyway, my em.mdp file is below. If I can get some suggestions on how to
more easily see my protein fluctuating to its minimized state, in vmd,
that would be great! Should I maybe use the .xtc trajectory file instead
of the .trr? Or should I add the lines nstvout or nstfout?
The .xtc will not be any different, and velocities and forces are not read by
VMD so they will not indicate anything.
You are probably experiencing absolutely normal behavior. If you want
fluctuation, run actual MD :)
-Justin
title = BR6_trp
cpp = /usr/bin/cpp
define = -DFLEXIBLE
constraints = none
integrator = steep
dt = 0.002 ; ps !
nsteps = 500
nstxout = 1
nstlist = 10
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
vdwtype = cut-off
rvdw = 0.9
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
Thanks in advance,
Halie Shah
University of Houston
Computational Biology Lab
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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