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This is wasting a large amount of CPU time.<br>Water is solid (ice) at 0 K.<br>A plain normal mode analysis would give you the normal modes of ice.<br>You can do a normal mode analysis of liquid water without minimization,<br>but the standard NMA techniques will not work.<br><br>Berk<br><br><hr id="stopSpelling">Date: Tue, 20 Oct 2009 18:33:43 +0530<br>From: simoniitchem@gmail.com<br>To: gmx-users@gromacs.org<br>Subject: [gmx-users] Normal mode analysis of pure water<br><br>Hi,<br> I encountered the following remarks during normal mode analysis of pure water. Can someone please suggest a solution.<br> mdrun_d -v -s water.tpr -o traj.trr -c confout.gro -e ener.edr -g md.log -mtx nm.mtx<br>Getting Loaded...<br>
Reading file water.tpr, VERSION 4.0.4 (double precision)<br>Loaded with Money<br><br>Non-cutoff electrostatics used, forcing full Hessian format.<br>Allocating Hessian memory...<br><br>starting normal mode calculation 'Pure Water'<br>
648 steps.<br><br>Maximum force: 2.74758e+03<br>Maximum force probably not small enough to ensure that you are in an<br>energy well. Be aware that negative eigenvalues may occur when the<br>resulting matrix is diagonalized.<br>
Finished step 648 out of 648<br><br>Writing Hessian...<br><br>gcq#258: "In the End Science Comes Down to Praying" (P. v.d. Berg)<br><br>g_nmeig_d -f nm.mtx -s water.tpr -of eigenfreq.xvg -ol eigenval.xvg -v eigenvec.trr<br>
<br>Reading file water.tpr, VERSION 4.0.4 (double precision)<br>Reading file water.tpr, VERSION 4.0.4 (double precision)<br>Reading double precision matrix generated by Gromacs VERSION 4.0.4<br>Full matrix storage format, nrow=1944, ncols=1944<br>
<br>Diagonalizing to find vectors 1 through 50...<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>
Writing eigenfrequencies - negative eigenvalues will be set to zero.<br><br>Writing average structure & eigenvectors 1--50 to eigenvec.trr<br><br>gcq#132: "Shit Happens" (Pulp Fiction)<br><br><br>The eigenfreq is 0 which is the problem<br>
<br>The .mdp file used was;<br>; User spoel (236)<br>; Wed Nov 3 17:12:44 1993<br>; Input file<br>;<br>cpp =<br>define = -DFLEXIBLE<br>constraints = none<br>integrator = nm<br>
nsteps = 10000<br>;<br>; Energy minimizing stuff<br>;<br>emtol = 0.01<br>emstep = 0.01<br>coulombtype = PME<br>nstcomm = 1<br>ns_type = grid<br>
rlist = 0.9<br>rcoulomb = 0.9<br>rvdw = 0.9<br>Tcoupl = no<br>Pcoupl = no<br>gen_vel = no<br><br><br><br><br> <br /><hr />What can you do with the new Windows Live? <a href='http://www.microsoft.com/windows/windowslive/default.aspx' target='_new'>Find out</a></body>
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