Jack Shultz wrote:
I should have included some output
Step= 32, Dmax= 2.4e-06 nm, Epot= -1.03223e+05 Fmax= 3.87326e+06, atom= 25439
Step= 33, Dmax= 1.2e-06 nm, Epot= -1.03222e+05 Fmax= 3.87334e+06, atom= 25439
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 10
Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)
writing lowest energy coordinates.
Steepest Descents converged to machine precision in 34 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -1.4354568e+06
Maximum force = 6.9535597e+10 on atom 25439
Norm of force = 4.5592896e+08
More details here.
http://www.hydrogenathome.org/result.php?resultid=1291344
From your pdb2gmx output, it looks like you have some lousy starting geometry
in whatever structure you're processing:
http://wiki.gromacs.org/index.php/Errors#Long_bonds_and.2For_missing_atoms
Try to run EM on that structure before solvating (i.e., in vacuo) , because you
probably have lots of steric clashes with the solvent arising because of
improper protein geometry.
-Justin
On Thu, Mar 12, 2009 at 10:59 AM, Jack Shultz
<jshu...@hydrogenathome.org> wrote:
Hi,
I think that my minimization are not running long enough. I've been
following the parameters in tutorials but it seems like they all die
at 34 steps
I've been using these tutorials
https://extras.csc.fi/chem/courses/gmx2007/tutorial1/tutorial1.pdf
http://md.chem.rug.nl/education/mdcourse/MDpract.html
Its been the same case for me regardless to whether I use Windows or
Linux platforms. Are there settings I can use to make the simulation
minimize longer or is this case where I need to have double precision
version?
--
Jack
http://www.facebook.com/home.php#/profile.php?id=832713248
http://hydrogenathome.org
--
========================================
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
========================================
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
