<br><br>
<div class="gmail_quote">On Tue, Feb 28, 2012 at 10:50 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote"><br><br>Steven Neumann wrote:
<div>
<div class="h5"><br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote"><br><br>On Tue, Feb 28, 2012 at 6:33 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br><br><br> Steven Neumann wrote:<br><br> I run energy minimization of my protein with implicit solvent:<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<br> 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> 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> Can you please explain?<br><br><br> 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<br> the cluster on a specific node<br></blockquote><br></div></div>Doesn't answer the question, but I'll assume CPU since EM doesn't work on GPU's. Just checking.
<div class="im"><br><br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote"> 4. Does an in vacuo minimization work (i.e., just turn off the GB<br> parts)? - yes, it works<br><br></blockquote>
<br></div>And what is the output?<br><br>In any case, I can't reproduce any problem doing EM with implicit solvent in 4.5.4 - my test systems work quite well. It may just be that the system cannot be minimized because of some clash that is unfavorable in an implicit solvent environment (thus causing an immediate halt, though that would be odd) but can be resolved in vacuo. Try using the structure produced by in vacuo minimization as input into the implicit solvent EM to see if this may be the case.
<div class="im"><br><br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote"><br>What shoould be the value for emtol in implicit solvent model with protein with app. 150 residues?<br><br></blockquote>
<br></div>One that is sufficient for the inherent forces in the system and for your application ;) I don't think there are any hard and fast rules here for standard MD, and the target is not dictated by the size of the protein.
<div class="HOEnZb">
<div class="h5"><br><br>-Justin<br></div></div></blockquote>
<div> </div>
<div> </div>
<div>Thank you Justin.</div>
<div> </div>
<div>Mark, would you suggest equilibration e.g. for 1ns with no restraints and no constraints in implicic solvent with timestep =0.0005 and then run MD with implicit employing LINCS?</div>
<div> </div>
<div>Steven</div>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">
<div class="HOEnZb">
<div class="h5"><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" target="_blank" value="+15402319080">(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>
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