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On 22/05/2011 3:35 PM, sreelakshmi ramesh wrote:
<blockquote
cite="mid:BANLkTimOY9iY=4+S2ezP3S7aU-NHmppL8A@mail.gmail.com"
type="cite">my starting structure has just two atoms one Na and
one Cl and they are seperated by a distance of 3 angstroms.Its not
a huge system.<br>
</blockquote>
<br>
So how come you have water molecules?<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:BANLkTimOY9iY=4+S2ezP3S7aU-NHmppL8A@mail.gmail.com"
type="cite"><br>
<div class="gmail_quote">On Sun, May 22, 2011 at 10:30 AM, Mark
Abraham <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<div text="#000000" bgcolor="#ffffff">
<div class="im"> On 22/05/2011 2:43 PM, sreelakshmi ramesh
wrote:
<blockquote type="cite">Dear gmx-users,<br>
I have a problem during
minimization and shows a error that water molecules
starting at atom X cannot be settled i had attached the
output of mdrun below. I read the earlier post for same
problem faced by other gmx users.tried to reduce the
timestep still facing the same error.Tried diff water
model and force fields as well to check if i get the
same error .But still irrespective of any water model
and forcefield i get the same error.And was not able
to find a solution.Any suggestion please....<br>
</blockquote>
<br>
</div>
Several people have suggested you may have a bad starting
structure, with atoms overlapping or such. This confirms it.<br>
<font color="#888888"> <br>
Mark</font>
<div>
<div class="h5"><br>
<br>
<blockquote type="cite"><font size="4"><b>OUTPUT OF
MDRUN</b><br>
</font><br>
Back Off! I just backed up md.log to ./#md.log.1#<br>
Reading file em.tpr, VERSION 4.5.3 (single precision)<br>
Starting 2 threads<br>
Making 1D domain decomposition 2 x 1 x 1<br>
<br>
Back Off! I just backed up em.trr to ./#em.trr.1#<br>
<br>
Back Off! I just backed up em.edr to ./#em.edr.1#<br>
<br>
Steepest Descents:<br>
Tolerance (Fmax) = 1.00000e+02<br>
Number of steps = 200000<br>
<br>
step 7: Water molecule starting at atom 7619 can not
be settled.<br>
Check for bad contacts and/or reduce the timestep if
appropriate.<br>
<br>
step 7: Water molecule starting at atom 3547 can not
be settled.<br>
Check for bad contacts and/or reduce the timestep if
appropriate.<br>
Wrote pdb files with previous and current coordinates<br>
Wrote pdb files with previous and current coordinates<br>
<br>
step 12: Water molecule starting at atom 7619 can not
be settled.<br>
Check for bad contacts and/or reduce the timestep if
appropriate.<br>
Wrote pdb files with previous and current coordinates<br>
<br>
step 17: Water molecule starting at atom 8007 can not
be settled.<br>
Check for bad contacts and/or reduce the timestep if
appropriate.<br>
Wrote pdb files with previous and current coordinates<br>
<br>
step 22: Water molecule starting at atom 8511 can not
be settled.<br>
Check for bad contacts and/or reduce the timestep if
appropriate.<br>
Wrote pdb files with previous and current coordinates<br>
<br>
Stepsize too small, or no change in energy.<br>
Converged to machine precision,<br>
but not to the requested precision Fmax < 100<br>
<br>
Double precision normally gives you higher accuracy.<br>
You might need to increase your constraint accuracy,
or turn<br>
off constraints alltogether (set constraints = none in
mdp file)<br>
<br>
writing lowest energy coordinates.<br>
<br>
Back Off! I just backed up confout.gro to
./#confout.gro.1#<br>
<br>
Steepest Descents converged to machine precision in 40
steps,<br>
but did not reach the requested Fmax < 100.<br>
Potential Energy = 2.4059008e+07<br>
Maximum force = 2.8605226e+08 on atom 8511<br>
Norm of force = 3.7174682e+06<br>
<br>
gcq#324: "Your Country Raised You, Your Country Fed
You, and Just Like Any Other Country it Will Break
You" (Gogol Bordello)<br>
<br>
</blockquote>
<br>
</div>
</div>
</div>
<br>
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</blockquote>
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<br>
</blockquote>
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