<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><br>Dear Ran,<br><br>I ran the whole NMA again and I found where I go wrong. I hope it will help others as well.<br>(sorry for a big email)<br><br><br>In steps 1 & 2 (of minimization) I kept the C-alpha frozen.<br><br>1. doublegrompp -f em1.mdp -c r1dodecapdb.pdb -p r1top.top -o em1tpr.tpr<br>mpirun -np 8 ~/gmxdpr/bin/doublemdrun -v -deffnm em1tpr<br><br>Steepest Descents converged to Fmax < 100 in 2569 steps<br>Potential Energy = -6.21296128286120e+03<br>Maximum force = 9.87358378592302e+01 on atom 701<br>Norm of force = 1.04875323563923e+01<br><br>2. doublegrompp -f em2.mdp -c em1tpr.gro -p r1top.top -o em2tpr.tpr -t em1tpr.trr<br>mpirun -np 8 ~/gmxdpr/bin/doublemdrun -v -deffnm em2tpr<br><br>Polak-Ribiere Conjugate Gradients converged to Fmax < 1 in 6596 steps<br>Potential
Energy = -7.56682084795001e+03<br>Maximum force = 9.92719787231560e-01 on atom 1320<br>Norm of force = 6.47772253797808e-02<br><br>3. doublegrompp -f em3.mdp -c em2tpr.gro -p r1top.top -o em3tpr.tpr -t em2tpr.trr<br>mpirun -np 8 ~/gmxdpr/bin/doublemdrun -v -deffnm em3tpr<br><br>Stepsize too small, or no change in energy.<br>Converged to machine precision,<br>but not to the requested precision Fmax < 10<br><br>writing lowest energy coordinates.<br><br>Steepest Descents converged to machine precision in 3018 steps,<br>but did not reach the requested Fmax < 10.<br>Potential Energy = -8.49398064549505e+03<br>Maximum force = 6.86336687926682e+01 on atom 935<br>Norm of force = 7.15798864024085e+00<br><br><br>4. doublegrompp -f em4.mdp -c em3tpr.gro -p r1top.top -o em4tpr.tpr -t em3tpr.trr<br>mpirun -np 8
~/gmxdpr/bin/doublemdrun -v -deffnm em4tpr<br><br>Stepsize too small, or no change in energy.<br>Converged to machine precision,<br>but not to the requested precision Fmax < 0.01<br><br>writing lowest energy coordinates.<br><br><br>Polak-Ribiere Conjugate Gradients converged to machine precision in 21674 steps,<br>but did not reach the requested Fmax < 0.01.<br>Potential Energy = -9.66058047638671e+03<br>Maximum force = 1.49342602818840e+00 on atom 590<br>Norm of force = 1.86576579430541e-01<br><br><br>5.doublegrompp -f em5.mdp -c em4tpr.gro -p r1top.top -o em5tpr.tpr -t em4tpr.trr<br> ~/gmxdpr/bin/doublemdrun -v -deffnm em5tpr<br><br>Low-Memory BFGS Minimizer converged to machine precision in 10346 steps,<br>but did not reach the requested Fmax < 0.0001.<br>Potential Energy = -9.66337416273684e+03<br>Maximum force = 6.48625019025464e-04
on atom 581<br>Norm of force = 6.35632681200205e-05<br><br>6.doublegrompp -f em6.mdp -c em5tpr.gro -p r1top.top -o em6tpr.tpr -t em5tpr.trr<br><br>Low-Memory BFGS Minimizer converged to machine precision in 3316 steps,<br>but did not reach the requested Fmax < 1e-08.<br>Potential Energy = -9.66337416275038e+03<br>Maximum force = 6.48788529801368e-05 on atom 8<br>Norm of force = 6.56362137550289e-06<br><br>7. doublegrompp -f em7.mdp -c em6tpr.gro -p r1top.top -o em7tpr.tpr -t em6tpr.trr<br><br>Low-Memory BFGS Minimizer converged to machine precision in 7530 steps,<br>but did not reach the requested Fmax < 1e-08.<br>Potential Energy = -9.66337416275071e+03<br>Maximum force = 4.07762128402886e-07 on atom 10<br>Norm of force = 5.79534451487287e-08<br><br>8. doublegrompp -f em8.mdp -c
em7tpr.gro -p r1top.top -o em8tpr.tpr -t em7tpr.trr<br>Low-Memory BFGS Minimizer converged to Fmax < 1e-08 in 5840 steps<br>Potential Energy = -9.66337416275070e+03<br>Maximum force = 8.41750710592449e-09 on atom 521<br>Norm of force = 1.28889193955553e-09<br><br><br>NMA<br><br>9. doublegrompp -f nma.mdp -t em8tpr.trr -c em8tpr.gro -p r1top.top -o nmatpr.tpr<br>~/gmxdpr/bin/doublemdrun -v -deffnm nmatpr<br><br><br>(a sinlge processor)<br> ~/gmxdpr/bin/doublemdrun -v -deffnm nmatpr<br>it created only one nmatpr.mtx<br>Maximum force: 8.41751e-09<br>Finished step 1400 out of 1400<br><br>It creates the output nmatpr.mtx nmatpr.edr etc....<br><br>Now I delete all nma files<br>rm nmatpr.*<br><br><br>(4 processor)<br>mpirun -np 4 ~/gmxdpr/bin/doublemdrun -v -deffnm nmatpr<br>Maximum force: 8.41768e-09<br>Maximum force: 8.41768e-09<br>Maximum force: 8.41768e-09<br>Maximum force:
8.41768e-09<br>Finished step 1399 out of 1400<br><br>Writing Hessian...<br><br><br>Writing Hessian...<br><br><br>Writing Hessian...<br>Finished step 1400 out of 1400<br><br>Writing Hessian...<br><br>Back Off! I just backed up nmatpr.mtx to ./#nmatpr.mtx.2#<br><br>It gives me negative eigenvalues.<br><br>One would expect it should not create nmatpr.mtx.1 nmatpr.mtc.2 etc...since these files have been removed. Because it created multiple nmatpr.mtx file and backup one over another<br><br>I am not sure If the problem occurs with my system , but other MPIRUN (with mdrun) do not create such backup.<br><br>Best,<br>nahren<br><br><br>--- On <b>Wed, 7/28/10, Ran Friedman <i><r.friedman@bioc.uzh.ch></i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>From: Ran Friedman <r.friedman@bioc.uzh.ch><br>Subject: Re: [gmx-users] Entropy from NMA<br>To: "Discussion list for GROMACS users"
<gmx-users@gromacs.org><br>Date: Wednesday, July 28, 2010, 3:10 PM<br><br><div id="yiv1885163162">
p.s. How big is this negative value?<br>
<br>
Ran Friedman wrote:
<blockquote type="cite">
Hi,<br>
<br>
Can you post the exact commands you used for EM and NMA?<br>
<br>
Ran<br>
<br>
nahren manuel wrote:
<blockquote type="cite">
<table border="0" cellpadding="0" cellspacing="0">
<tbody>
<tr>
<td style="font-family: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; font-size: inherit; line-height: inherit; font-size-adjust: inherit; font-stretch: inherit;" valign="top">Dear Gromacs Users,<br>
<br>
I am trying to calculate Entropy from Normal Mode Analysis.<br>
I minimized the structure to<br>
8.41750710592449e-09<br>
<br>
Then I calculated the normal mode (the mdp file is given below). <br>
<br>
But when i try to calculate the Eigenvalues, I get the following warning<br>
<br>
<br>
One of the lowest 6 eigenvalues has a non-zero value.<br>
This could mean that the reference structure was not<br>
properly energy minimized.<br>
Writing eigenvalues...<br>
<br>
I get only negative eigenvalues.<br>
<br>
Let me also add that I used the same mdp file for minimization changing
the integrator to steep, cg and finally to l-bfgs.<br>
<br>
Best,<br>
nahren<br>
<br>
-----------------------<br>
integrator = nm <br>
constraints = none<br>
define = -DFLEXIBLE<br>
emtol = 0.00000001 <br>
emstep = 0.00000001 <br>
nsteps = 50000 <br>
nstlist = 1 <br>
ns_type = grid <br>
rlist = 1.5 <br>
coulombtype = shift <br>
rcoulomb-switch = 1.0 <br>
rvdw-switch = 1.0 <br>
vdwtype = shift<br>
rcoulomb = 1.3<br>
rvdw = 1.3</td>
</tr>
</tbody>
</table>
<br>
</blockquote>
<br>
<br>
<pre class="yiv1885163162moz-signature">-- <br>------------------------------------------------------<br>Ran Friedman<br>Postdoctoral Fellow<br>Computational Structural Biology Group (A. Caflisch)<br>Department of Biochemistry<br>University of Zurich<br>Winterthurerstrasse 190<br>CH-8057 Zurich, Switzerland<br>Tel. +41-44-6355559<br>Email: <a rel="nofollow" class="yiv1885163162moz-txt-link-abbreviated" ymailto="mailto:r.friedman@bioc.uzh.ch" target="_blank" href="/mc/compose?to=r.friedman@bioc.uzh.ch">r.friedman@bioc.uzh.ch</a><br>Skype: ran.friedman<br>------------------------------------------------------<br> </pre>
</blockquote>
<br>
<br>
</div><br>-----Inline Attachment Follows-----<br><br><div class="plainMail">-- <br>gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="/mc/compose?to=gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a></div></blockquote></td></tr></table><br>