[gmx-users] trajectory file not moving in vmd

Halie Shah haliepshah at gmail.com
Mon Apr 13 19:21:49 CEST 2009


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.

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.

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?

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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