<div dir="ltr">Hi Tianwu,<div style>just to be sure, can you try to compile with CMAKE_BUILD_TYPE=Debug</div><div style>and repeating again the runs?</div><div style><br></div><div style>Francesco</div></div><div class="gmail_extra">
<br><br><div class="gmail_quote">2013/6/13 Mark Abraham <span dir="ltr"><<a href="mailto:mark.j.abraham@gmail.com" target="_blank">mark.j.abraham@gmail.com</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr"><br><div class="gmail_extra"><br><br><div class="gmail_quote"><div class="im">On Wed, Jun 12, 2013 at 10:58 PM, Tianwu Zang <span dir="ltr"><<a href="mailto:tz4@rice.edu" target="_blank">tz4@rice.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi all,<div>I am using a very common system for testing, with only one protein (~1000+ atoms) and ~7000+ water atoms with box size = 4.5</div>
<div>When I tried rerun the simulation, results kept the same with the last run for the same kernel, but became quite different (even at step=0) for different kernel, like using generic kernel in the first run and specific kernel in the second run..</div>
<div>In my case, for specific kernel, f[0]~884 and for generic kernel f[0]~337, which is a huge difference..</div><div>I have already set the variable gen_seed in my .mdp file so there shouldn't be any problem of random seed.</div>
<div>Now I am wondering if these force results should not differ from each other, where I am doing wrong?</div></div></blockquote><div><br></div></div><div>OK. What's your .mdp file?</div><span class="HOEnZb"><font color="#888888"><div>
<br></div><div>
Mark</div></font></span><div><div class="h5"><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>Thanks again,</div><div>-Mark</div></div>
<div><div>
<div class="gmail_extra"><br><br><div class="gmail_quote">
On Wed, Jun 12, 2013 at 8:05 AM, francesco oteri <span dir="ltr"><<a href="mailto:francesco.oteri@gmail.com" target="_blank">francesco.oteri@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hi,<div>Marc said it is using -rerun and, as far as I know and basing on my experience, </div><div>it gives exactly the same reults. Of course, also the seed has to be the same :D</div><span><font color="#888888"><div>
<br></div><div>Francesco</div></font></span></div><div><div><div class="gmail_extra"><br><br><div class="gmail_quote">2013/6/12 Berk Hess <span dir="ltr"><<a href="mailto:hess@kth.se" target="_blank">hess@kth.se</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>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<div><div><br>
<br>
On 06/12/2013 01:50 PM, Mark Abraham wrote:<br>
</div></div></div><div><div>
<blockquote type="cite">
<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 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>That's better, but the advice here is worth
following: <a href="http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy" target="_blank">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>Describing in words what your system is doing
would be a good start ;-)</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">
<span><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>
<div>
<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 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 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 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 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><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 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 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">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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