<br><br><div class="gmail_quote">On Tue, Feb 28, 2012 at 6:33 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="HOEnZb"><div class="h5"><br>
<br>
Steven Neumann wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I run energy minimization of my protein with implicit solvent:<br>
<br>
constraints = none<br>
<br>
integrator = steep<br>
<br>
dt = 0.001 ; ps<br>
<br>
nsteps = 30000<br>
<br>
vdwtype = cut-off<br>
<br>
coulombtype = cut-off<br>
<br>
pbc = no<br>
<br>
nstlist = 0<br>
<br>
ns_type = simple<br>
<br>
rlist = 0 ; this means all-vs-all (no cut-off),<br>
<br>
which gets expensive for bigger systems<br>
<br>
rcoulomb = 0<br>
<br>
rvdw = 0<br>
<br>
comm-mode = angular<br>
<br>
comm-grps = Protein<br>
<br>
optimize_fft = yes<br>
<br>
;<br>
<br>
; Energy minimizing stuff<br>
<br>
;<br>
<br>
emtol =<br>
<br>
5.0<br>
<br>
emstep = 0.01<br>
<br>
;<br>
<br>
; Implicit solvent<br>
<br>
;<br>
<br>
implicit_solvent = GBSA<br>
<br>
gb_algorithm = OBC<br>
<br>
nstgbradii = 1<br>
<br>
rgbradii = 0 ; [nm] Cut-off for the calculation of the<br>
<br>
Born radii. Currently must be equal to rlist<br>
<br>
gb_epsilon_solvent = 80 ; Dielectric constant for the implicit solvent<br>
<br>
; gb_saltconc = 0 ; Salt concentration for implicit solvent<br>
<br>
models, currently not used<br>
<br>
sa_algorithm = Ace-approximation<br>
<br>
sa_surface_tension = 2.25936<br>
<br>
And I obtained:<br>
<br>
Steepest Descents:<br>
<br>
Tolerance (Fmax) = 1.00000e+03<br>
<br>
Number of steps = 30000<br>
<br>
Step Time Lambda<br>
<br>
0 0.00000 0.00000<br>
<br>
<br>
<br>
Steepest Descents converged to Fmax < 1000 in 1 steps<br>
<br>
Potential Energy = inf<br>
<br>
Maximum force = 0.0000000e+00 on atom 0<br>
<br>
Norm of force = nan<br>
<br>
<br>
Can you please explain?<br>
<br>
</blockquote>
<br></div></div>
Not without more information.<br>
<br>
1. What is in the system? - protein without specified box<br>
2. Which version of Gromacs is this? - Gromacs 4.5.4<br>
3. Are you using GPU or CPU architecture? - I run it straight from the cluster on a specific node<br>
4. Does an in vacuo minimization work (i.e., just turn off the GB parts)? - yes, it works</blockquote><div><br>What shoould be the value for emtol in implicit solvent model with protein with app. 150 residues?<br><br>Thank you,<br>
<br>Steven <br></div><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><span class="HOEnZb"><font color="#888888"><br>
<br>
-Justin</font></span><div class="HOEnZb"><div class="h5"><br>
<br>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
==============================<u></u>==========<br>
-- <br>
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