francesca vitalini wrote:
I achieve
Steepest Descents converged to machine precision in 205 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -1.49131940478719e+07
Maximum force = 1.09664530279637e+06 on atom 1520 (parto of the
protein)
Norm of force = 2.28369808518165e+06
The magnitude of the force suggests atomic overlap somewhere. Start by
investigating the environment around atom 1520.
and the system looked with vmd doesn't look as if it was exploding.
However, I have warnings about the table extension and I don't know why
but gromacs writes pdb files sometime. However I thought that there
The "step.pdb" files are written when mdrun is about to crash.
might have been an error in the way I defined the position restraints,
in fact in the mdp file I hade define = -DEPOSRE while in the topology I
had ifdef DEFINE_WAT, so it might have moved it all without fixing the
water. So I tried again and this time I got
The "define" statements are literal, so be careful of typos. -DEPOSRE will not
work when the topology calls for -DPOSRES. So unless you've changed default
naming for "define" statements, you're not going to get what you expect.
Steepest Descents converged to machine precision in 72 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -2.0135496e+07
Maximum force = 2.0486184e+12 on atom 4479
Norm of force = 7.2424045e+13
Again, symptomatic of severe atomic overlap.
but again the same issue with table extent and still the production of
pdb files.
Any explanations?
Investigate the starting configurations near the problematic atoms.
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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