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Hi Berk,<br>
<br>
I've reconfigured and recompiled today, but I think this is due to
older modifications. I'm fighting with these issues for a week or so,
and until today was certain that there was something wrong in the
structure I was simulating.<br>
<br>
I don't have 4.0.5 handy but with 4.0.2 everything works fine.<br>
<br>
Thanks,<br>
Ran.<br>
<br>
Berk Hess wrote:
<blockquote cite="mid4AC9FDA8.3050402@cbr.su.se" type="cite">
<pre wrap="">Hi,
Did you try to rerun configure and recompile everything?
I just compared EM to an older version and got exactly the same results.
Berk
Jochen Hub wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi Ran,
did you also have these problems only during energy minimization? I
asking since I want to use the present git for longer production runs?
Best,
Jochen
Ran Friedman wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi,
I'm fighting these issues as well.
With the new git version I either get a segfault or really unrealistic
structures. For example, I saw that a hydrogen bound to nitrogen near a
C-terminal carboxylate group was located at the same place of a
carboxylate oxygen (!) following minimisation. As this happened in more
than one structure I guess something is broken. It's as if minimisation
doesn't take the LJ parameters into account.
Ran.
Jochen Hub wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi,
mdrun of the present git version stops during energy minimization in
Segfaul/Bus error on my Mac. Gromacs 405 from a few weeks ago works
fine with the same tpr and the same configure options. gdb reports
some error in the assembly loops, I am not sure what the error means
however:
gcc version 4.0.1 (Apple Inc. build 5490)
-------------------------------------------
Program received signal EXC_BAD_INSTRUCTION, Illegal
instruction/operand.
_nb_kernel_ia32_3dnow_test_asm () at nb_kernel_ia32_3dnow_test_asm.s:23
23 nb_kernel_ia32_3dnow_test_asm.s: No such file or directory.
in nb_kernel_ia32_3dnow_test_asm.s
(gdb) bt
#0 _nb_kernel_ia32_3dnow_test_asm () at
nb_kernel_ia32_3dnow_test_asm.s:23
#1 0x002682a0 in nb_kernel_ia32_3dnow_test (log=0xa08834c0) at
nb_kernel_ia32_3dnow.c:186
#2 0x0026831f in nb_kernel_setup_ia32_3dnow (log=0xa08834c0,
list=0x804200) at nb_kernel_ia32_3dnow.c:212
#3 0x00268bb2 in gmx_setup_kernels (fplog=0xa08834c0) at
nonbonded.c:248
#4 0x00057899 in init_forcerec (fp=0xa08834c0, fr=0x81d000,
fcd=0x503130, ir=0x801a00, mtop=0x501860, cr=0x500330, box=0xbfffd76c,
bMolEpot=0, tabfn=0x500590 "table.xvg", tabpfn=0x5005b0 "tablep.xvg",
tabbfn=0x5005d0 "table.xvg", bNoSolvOpt=0, print_force=-1) at
force.c:1436
#5 0x00012529 in mdrunner (fplog=0xa08834c0, cr=0x500330, nfile=27,
fnm=0x2a06c0, bVerbose=1, bCompact=1, ddxyz=0xbfffe8e0,
dd_node_order=1, rdd=0, rconstr=0, dddlb_opt=0x2801b1 "auto",
dlb_scale=0.800000012, ddcsx=0x0, ddcsy=0x0, ddcsz=0x0, nstepout=100,
ed=0x0, repl_ex_nst=0, repl_ex_seed=-1, pforce=-1, cpt_period=15,
max_hours=-1, Flags=7168) at md.c:305
#6 0x00018ce0 in main (argc=6, argv=0xbfffe94c) at mdrun.c:496
Current language: auto; currently asm
Newer gccs (4.2 or 4.4) did not help. Compiling in 64bit did not help
either.
Any suggestions?
Thanks a lot,
Jochen
</pre>
</blockquote>
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<pre wrap="">
</pre>
</blockquote>
<pre wrap=""><!---->
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<br>
<br>
<pre class="moz-signature" cols="72">--
------------------------------------------------------
Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355559
Email: <a class="moz-txt-link-abbreviated" href="mailto:r.friedman@bioc.unizh.ch">r.friedman@bioc.unizh.ch</a>
Skype: ran.friedman
------------------------------------------------------
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