[gmx-users] trajectory file not moving in vmd

[Justin A. Lemkul]

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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