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<div class="moz-cite-prefix">Hi,<br>
<br>
You haven't said at what step this happens.<br>
At step zero the forces should match, except for the last
decimal(s).<br>
But since MD is chaotic, trajectories diverge exponentially, which
is very fast.<br>
This usually means forces are significantly decorrelated after 100
to 1000 steps.<br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
On 06/12/2013 01:50 PM, Mark Abraham wrote:<br>
</div>
<blockquote
cite="mid:CAMNuMAQ0vcscwJricaQUci4mU-XG3-dgz9ksAbwB9Em3-AyZuw@mail.gmail.com"
type="cite">
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<div dir="ltr"><br>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Wed, Jun 12, 2013 at 3:28 AM, Mark
Tianwu Zang <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:zangtw@gmail.com" target="_blank">zangtw@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div dir="ltr"><span
style="font-family:arial,sans-serif;font-size:13px">Hi
Francesco and Mark,</span>
<div style="font-family:arial,sans-serif;font-size:13px">
Thanks for your precious advice. Now this time I
didn't insert any code but use the .mdp options
instead. I used the following steps: first set the
environment variable GMX_NB_GENERIC=1, run the
GROMACS, and run again with the same input but
GMX_NB_GENERIC unset. Next, compare two force.xvg
generated from two traj.trr using g_traj. However, I
still found the results different from each other.. My
gcc version is 4.6.3(almost the newest), my fftw
version is 3.3.3(double precision, and GROMACS is also
build in double-precision) and I use the argument
--reprod to make sure the calculation of PME is
reproducible. </div>
<div style="font-family:arial,sans-serif;font-size:13px">My
running command for GROMACS is</div>
<div style="font-family:arial,sans-serif;font-size:13px">mpirun
-np 2 mdrun_mpi -s test.tpr -v -reprod</div>
</div>
</blockquote>
<div><br>
</div>
<div style="">That's better, but the advice here is worth
following: <a moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy">http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy</a></div>
<div> </div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div dir="ltr">
<div style="font-family:arial,sans-serif;font-size:13px">
I tried to attach my test tpr and mdp file in this
email but my attempt was not approved by administrator
because the email would be oversized..</div>
</div>
</blockquote>
<div><br>
</div>
<div style="">Describing in words what your system is doing
would be a good start ;-)</div>
<div><br>
</div>
<div style="">Mark</div>
<div style=""><br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
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<div dir="ltr">
<span class=""><font color="#888888">
<div
style="font-family:arial,sans-serif;font-size:13px"><br>
</div>
<div
style="font-family:arial,sans-serif;font-size:13px">
-Mark</div>
</font></span></div>
<div class="">
<div class="h5">
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Sat, Jun 8, 2013 at 7:25
AM, francesco oteri <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:francesco.oteri@gmail.com"
target="_blank">francesco.oteri@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0px
0px 0px
0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div dir="ltr">In my case the excuse was that
the system administrator never updated the
compiler.
<div>
So I after a couple of days I installed the
new compiler.</div>
<div>In any case, I noticed that the
problem disappeared using the "Debug"
version so I guess </div>
<div>it is something related either to the
optimized kernel or the optimization
strategy used by the compiler. </div>
<span><font color="#888888">
<div><br>
</div>
<div><br>
</div>
<div>Francesco</div>
</font></span></div>
<div>
<div>
<div class="gmail_extra">
<br>
<br>
<div class="gmail_quote">2013/6/8 Mark
Abraham <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:mark.j.abraham@gmail.com"
target="_blank">mark.j.abraham@gmail.com</a>></span><br>
<blockquote class="gmail_quote"
style="margin:0px 0px 0px
0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div dir="ltr"><br>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">
<div>On Sat, Jun 8, 2013 at
12:59 PM, francesco oteri <span
dir="ltr"><<a
moz-do-not-send="true"
href="mailto:francesco.oteri@gmail.com"
target="_blank">francesco.oteri@gmail.com</a>></span>
wrote:<br>
<blockquote
class="gmail_quote"
style="margin:0px 0px 0px
0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div dir="ltr">H Mark,
<div>I had a similar
problem recently and,
eventually, I figured
out the cause was the
compiler version.</div>
<div>I was using gcc4.1
and my problem got
solved using a more
recent version.
Actually, this issue </div>
<div>in the website is
clearly stated. So,
which compiler are you
using?</div>
<div>Could you report an
example
of inconsistency?</div>
</div>
</blockquote>
<div><br>
</div>
</div>
<div>That warning has been there
many years, but AFAIK nobody
ever identified the real
problem (if it exists).
Nevertheless, there is no
excuse for using both GROMACS
and such an old compiler! :-)</div>
<span><font color="#888888">
<div><br>
</div>
<div>Mark</div>
</font></span>
<div>
<div>
<div><br>
</div>
<blockquote
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style="margin:0px 0px 0px
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<div dir="ltr">
<div><br>
</div>
<div>Francesco </div>
</div>
<div class="gmail_extra">
<div>
<div>
<br>
<br>
<div
class="gmail_quote">2013/6/8
Mark Abraham <span
dir="ltr"><<a
moz-do-not-send="true" href="mailto:mark.j.abraham@gmail.com"
target="_blank">mark.j.abraham@gmail.com</a>></span><br>
<blockquote
class="gmail_quote"
style="margin:0px
0px 0px
0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div dir="ltr"><br>
<div
class="gmail_extra"><br>
<br>
<div
class="gmail_quote">On
Sat, Jun 8,
2013 at 1:44
AM, Mark
Tianwu Zang <span
dir="ltr"><<a
moz-do-not-send="true" href="mailto:zangtw@gmail.com" target="_blank">zangtw@gmail.com</a>></span>
wrote:<br>
<blockquote
class="gmail_quote"
style="margin:0px
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<div dir="ltr">Dear
all,
<div>I have
inserted only
a few lines
after update()
in md.c to
monitor how
forces change
after every
step. My codes
are very
simple, just
like:</div>
<div> </div>
<div>for i=0
to
md->nalloc</div>
<div>
<div> fprintf
f[i][0],
f[i][1],
f[i][2]</div>
</div>
</div>
</blockquote>
<div><br>
</div>
<div>That
seems like the
hard way to do
it, with
nstfout
available in
the .mdp
file. </div>
<div><br>
</div>
<blockquote
class="gmail_quote"
style="margin:0px
0px 0px
0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div dir="ltr">
<div>
<div>However,
I found the
results of my
output become
quite
different
after
exporting
GMX_NB_GENERIC=1,
which means
the forces
calculated by
generic kernel
and
interaction-specific
kernel are not
the same. I am
a little
confused now..
It this
phenomena
quite normal
or I ignored
something
important?</div>
</div>
</div>
</blockquote>
<div><br>
</div>
<div>AFAIK the
generic kernel
should serve
as a reference
for the
interaction-specific
kernels. If
not, there
might a
problem to
fix. Hard to
say without
context.</div>
<div><br>
</div>
<div>Mark</div>
<div><br>
</div>
<blockquote
class="gmail_quote"
style="margin:0px
0px 0px
0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div dir="ltr">
<div>
<div>Thanks a
lot!</div>
<span><font
color="#888888">
<div>-Mark</div>
<div><br>
</div>
</font></span></div>
<div><br>
</div>
</div>
<span><font
color="#888888">
<br>
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<span><font
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Cordiali saluti,
Dr.Oteri Francesco
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