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On 22/05/2011 4:54 PM, sreelakshmi ramesh wrote:
<blockquote
cite="mid:BANLkTinGpdWCxHNykwqBTn-WPGGfq9Jwxg@mail.gmail.com"
type="cite">ya sorry i actually meant to say that the starting pdb
file had just NA and Cl.I then solvated it with tip4p water.Anad
then try to minimize it.<br>
</blockquote>
<br>
Then you must have done it wrong. Follow along the workflow of a
tutorial. Maybe your ion atom types do not match the names in the
VDW radii database and that is generating atom clashes. See genbox
-h<br>
<br>
When asking for help give complete descriptions and exact commands
copied from your terminal. Nobody's got the time to solve your
problem except you, but if you want someone else's insight for free,
you need to give them all the data you think might even possibly be
relevant. They aren't going to bother asking questions to get data
that you could have already provided...<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:BANLkTinGpdWCxHNykwqBTn-WPGGfq9Jwxg@mail.gmail.com"
type="cite">
<div class="gmail_quote">On Sun, May 22, 2011 at 11:59 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 3:35 PM, sreelakshmi ramesh
wrote:
<blockquote 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>
</div>
So how come you have water molecules?<br>
<font color="#888888"> <br>
Mark</font>
<div>
<div class="h5"><br>
<br>
<blockquote 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"
target="_blank">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> 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><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>
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