Mark, hello!<br><br>I think that there is some error durins saving of my minimization data<br><br>As the result of the minimization I've obtained <br><br>(1)<br>Low-Memory BFGS Minimizer converged to machine precision in 3723 steps,<br>
but did not reach the requested Fmax < 0.<br>Potential Energy = 2.08789280994511e+03<br>Maximum force = 3.01715687185776e-04 on atom 58<br>Norm of force = 3.09301310600005e-05<br><br>So the Fmax is sufficient low<br>
<br>But when I've load this data for NMA I've obtained<br><br>(2)<br>Maximum force: 8.41270e+02<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><br><br>So the Fmax is indeed very big for NMA but why it's not the same as in the (1)?<br><br>This is my script for NMA wich indicate that I've load to NMA suitable data<br><br>
# Steep <br>grompp_d -f minimSTEEP.mdp -c conf_newbox.gro -p topol.top -o minimizedS.tpr<br><br>mdrun_d -v -deffnm minimizedS<br><br><br># Grad<br>grompp_d -f minimGRAD.mdp -c minimizedS.gro -p topol.top -o minimizedGRAD.tpr<br>
<br>mdrun_d -v -deffnm minimizedGRAD<br><br><br># NMA<br>grompp_d -f nma.mdp -c minimizedGRAD.tpr -p topol.top -o fornma.tpr<br><br>mdrun_d -v -deffnm fornma -mtx nm.mtx<br><br><br><br><br>Where is the error?<br><br><br>James<br>
<br><br><div class="gmail_quote">2011/10/28 Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div bgcolor="#FFFFFF" text="#000000"><div><div></div><div class="h5">
On 28/10/2011 2:30 AM, James Starlight wrote:
<blockquote type="cite">That's energy ouptut from minimization with that
parametries ( there is also 1 step of steep minimization before
that )<br>
<br>
integrator = l-bfgs<br>
emtol = 0.001 <br>
emstep = 0.001 ; Energy step size<br>
nsteps = 5000000000 ; Maximum number of
(minimization) steps to perform<br>
<br>
<br>
; Parameters describing how to find the neighbors of each atom and
how to calculate the interactions<br>
nstlist = 1 ; Frequency to update the neighbor list
and long range forces<br>
ns_type = grid ; Method to determine neighbor list
(simple, grid)<br>
rlist = 1.2 ; Cut-off for making neighbor list
(short range forces)<br>
coulombtype = Shift <br>
rcoulomb = 1.0<br>
rcoulomb_switch = 0.7<br>
vdwtype = Shift<br>
rvdw = 1.0<br>
rvdw_switch = 0.7<br>
<br>
<br>
Output:<br>
<br>
Low-Memory BFGS Minimizer converged to Fmax < 0.001 in 3646
steps<br>
Potential Energy = 2.28946300988746e+03<br>
Maximum force = 8.47298141911052e-04 on atom 100<br>
Norm of force = 3.90346504086500e-04<br>
<br>
I'm not sure about the succses of that minimization due to the big
Epot. <br>
<br>
<fieldset></fieldset>
<br>
</blockquote>
<br></div></div>
You look like you are shuffling deck chairs on the Titanic. I
suggested you actually go and visualize your input and output
trajectories. Sadly that doesn't seem to have happened.<br><font color="#888888">
<br>
Mark<br>
</font></div>
<br>--<br>
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