[gmx-developers] Segfault during EM in recent git version
Jochen Hub
jochen at xray.bmc.uu.se
Wed Oct 7 12:54:03 CEST 2009
David van der Spoel wrote:
> Berk Hess wrote:
>> Hi,
>>
>> Steepest descents does run without too many Lincs warnings.
>> I don't see why you would want to run conjugate gradients on a protein
>> in water.
>> But if cg runs without virtual sites, it should also run with virtual
>> sites.
>> Have you checked if the same system does miminize properly with cg
>> without
>> virtual sites, but with constraints?
>
> And are you using aromatic v-sites? or just hydrogens?
I am only using hydrogen v-sites.
>>
>> Berk
>>
>> Jochen Hub wrote:
>>> Hey Berk, thanks for your patience. I have already tried with
>>> constraints, but then other problems occur. Now I have been trying cg
>>> with
>>>
>>> constraints = all-bonds
>>> constraint-algorithm = Lincs
>>> lincs-order = 8
>>> lincs-iter = 6
>>>
>>> As a result, the EM seems fine for 30 steps, then the rings start to
>>> be distorted. Within 2 steps, Tyr and Phe rings are not planar any
>>> more (and look pretty much like a sugar ring), and a few steps later
>>> the rings explode.
>>>
>>> I have played a bit with lincs-order and iter, steep instead of
>>> conjugate gradient, and emstep, but it did not improve things. Lincs
>>> warings with large angles (50-100 degree) always occur, and sometimes
>>> the EM breaks up because of more than 1000 lincs warnings.
>>>
>>> Jochen
>>>
>>>
>>>
>>> Berk Hess wrote:
>>>> Ah, the explanation is much simpler.
>>>> You should never use the vsite constructions in proteins without all
>>>> bonds constrained.
>>>> grompp does not check for this and it would be difficult to implement.
>>>> We could consider having pdb2gmx replace all bonds by constraints
>>>> when you ask for virtual sites.
>>>>
>>>> The actual problem is only in tetrahedral hydrogens in CH2 groups,
>>>> which are constructed using a non-normalized linear combinations and
>>>> cross product.
>>>> Even with all bonds constrained, this makes the hydrogen position
>>>> fluctuate a few percent
>>>> from the intended position.
>>>>
>>>> Berk
>>>>
>>>> Jochen Hub wrote:
>>>>
>>>>> Berk Hess wrote:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> I think this is "normal".
>>>>>> It could be that with vsites you get such warnings easier, since the
>>>>>> distance between
>>>>>> the two masses is small and in EM displacement is directly
>>>>>> proportional
>>>>>> to the force
>>>>>> (no mass factor), so the rotation will be larger than without
>>>>>> vsites.
>>>>>>
>>>>>>
>>>>> Hi,
>>>>>
>>>>> Here's some more news on the lincs warnings. Please have a look at
>>>>> his
>>>>> shapshot series:
>>>>>
>>>>> http://xray.bmc.uu.se/~jochen/lyp.jpg
>>>>>
>>>>> Snapshot 2 (EM step 28) is right after the first one (EM step 27) and
>>>>> caused the first lincs warning. EM steps 1-27 look just fine.
>>>>> Apparently, the lincs warnings in the lysine tip are rather a side
>>>>> effect of wrong C-H bond lengths along the lysine side chain. A few
>>>>> steps later, the C-H bonds are starting to fluctuate, and finally the
>>>>> EM crashes (sometimes again with a Segfault), or it hangs.
>>>>>
>>>>> In addition, I am also getting weired lincs warnings with
>>>>> rotations of
>>>>> exactly (!) 90 degree:
>>>>>
>>>>> atom 1 atom 2 angle previous, current, constraint length
>>>>> 247 250 90.0 0.1635 8.3257 0.1635
>>>>> 247 251 90.0 0.1635 7.3325 0.1635
>>>>> 250 251 90.0 0.0922 6.1981 0.0922
>>>>> 886 889 90.0 0.1583 0.6672 0.1583
>>>>> 886 890 90.0 0.1582 0.6672 0.1583
>>>>> 889 890 90.0 0.0802 0.3093 0.0802
>>>>> 1291 1294 90.0 0.1583 0.4725 0.1583
>>>>> 1291 1295 90.0 0.1582 0.4725 0.1583
>>>>> 1294 1295 90.0 0.0802 0.2394 0.0802
>>>>> 1513 1516 40.2 0.1583 0.1586 0.1583
>>>>> 1513 1517 39.9 0.1583 0.1578 0.1583
>>>>> 1516 1517 38.7 0.0802 0.0802 0.0802
>>>>>
>>>>> That does not look like coincidence, I strongly feel there is
>>>>> something wrong with the construction of the vsites?
>>>>>
>>>>> Jochen
>>>>>
>>>>>
>>>>>
>>>>>> Berk
>>>>>>
>>>>>> Jochen Hub wrote:
>>>>>>
>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> this fixes the Segfault, thanks! However, there are still LINCS
>>>>>>> warnings in the lysines, and sometimes also at isoleucines and
>>>>>>> at the
>>>>>>> OH-group of Tyr. Typically after 20-40 EM steps which look fine
>>>>>>> according to the decreasing Fmax etc. They always appear if the the
>>>>>>> cases with C in one cg, and the 2 heavy vsites plus one vsite
>>>>>>> (such as
>>>>>>> N) together in one cg:
>>>>>>>
>>>>>>> 1291 amber99_11 80 LYP CE 1189 -0.0143
>>>>>>> 14.026 ;
>>>>>>> qtot -4.006
>>>>>>> 1292 amber99_28 80 LYP HE1 1190 0.1135
>>>>>>> 0 ;
>>>>>>> qtot -3.893
>>>>>>> 1293 amber99_28 80 LYP HE2 1191 0.1135
>>>>>>> 0 ;
>>>>>>> qtot -3.779
>>>>>>> 1294 MNH3 80 LYP MNZ1 1192 0
>>>>>>> 8.517 ;
>>>>>>> qtot -3.779
>>>>>>> 1295 MNH3 80 LYP MNZ2 1192 0
>>>>>>> 8.517 ;
>>>>>>> qtot -3.779
>>>>>>> 1296 amber99_39 80 LYP NZ 1192 -0.3854
>>>>>>> 0 ;
>>>>>>> qtot -4.165
>>>>>>> 1297 amber99_17 80 LYP HZ1 1193 0.34
>>>>>>> 0 ;
>>>>>>> qtot -3.825
>>>>>>> 1298 amber99_17 80 LYP HZ2 1194 0.34
>>>>>>> 0 ;
>>>>>>> qtot -3.485
>>>>>>> 1299 amber99_17 80 LYP HZ3 1195 0.34
>>>>>>> 0 ;
>>>>>>> qtot -3.145
>>>>>>>
>>>>>>> Where the warning looks like that:
>>>>>>>
>>>>>>> bonds that rotated more than 30 degrees:
>>>>>>> atom 1 atom 2 angle previous, current, constraint length
>>>>>>> 1291 1294 36.8 0.1583 0.1576 0.1583 -> C--MNH3
>>>>>>> 1291 1295 37.6 0.1583 0.1587 0.1583 -> C--MNH3
>>>>>>> 1294 1295 35.4 0.0802 0.0805 0.0802 -> MNH3-MNH3
>>>>>>>
>>>>>>> Cheers,
>>>>>>> Jochen
>>>>>>>
>>>>>>>
>>>>>>> hess at sbc.su.se wrote:
>>>>>>>
>>>>>>>> Ah, this is in the vsite fix I made for the bug you
>>>>>>>> reported previously.
>>>>>>>> This code is quite obviously incorrect.
>>>>>>>> But I realize now it can be done simpler.
>>>>>>>> if (atom[a].ptype != eptVSite || pbc_set[a]) {
>>>>>>>> can be replaced by
>>>>>>>> if (pbc_set[a]) {
>>>>>>>>
>>>>>>>> This will certainly solve your last crash.
>>>>>>>> Just to be sure, could you check that this still fixes
>>>>>>>> the bug you reported previously?
>>>>>>>>
>>>>>>>> Berk
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>> Sorry, here a few more details:
>>>>>>>>>
>>>>>>>>> (gdb) list
>>>>>>>>> 1498 }
>>>>>>>>> 1499 if (vsite_pbc_f[vsi] == -1) {
>>>>>>>>> 1500 /* Check if this is the first processed atom
>>>>>>>>> of a
>>>>>>>>> vsite only cg */
>>>>>>>>> 1501 bViteOnlyCG_and_FirstAtom = TRUE;
>>>>>>>>> 1502 for(a=cgs->index[cg_v]; a<cgs->index[cg_v+1];
>>>>>>>>> a++) {
>>>>>>>>> 1503 if (atom[a].ptype != eptVSite ||
>>>>>>>>> pbc_set[a]) {
>>>>>>>>> 1504 bViteOnlyCG_and_FirstAtom = FALSE;
>>>>>>>>> 1505 break;
>>>>>>>>> 1506 }
>>>>>>>>> 1507 }
>>>>>>>>>
>>>>>>>>> The problem is that the atom[a=0] is not defined.
>>>>>>>>>
>>>>>>>>> Jochen
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Berk Hess wrote:
>>>>>>>>>
>>>>>>>>>> Jochen Hub wrote:
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> Berk Hess wrote:
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>> Did you use cut-off's?
>>>>>>>>>>>> New all-versus-all loops have been added for simulations
>>>>>>>>>>>> without
>>>>>>>>>>>> cut-off's.
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>> Yes, for both coulomb and vdw:
>>>>>>>>>>>
>>>>>>>>>>> coulombtype = Cut-off
>>>>>>>>>>> vdw-type = Cut-off
>>>>>>>>>>>
>>>>>>>>>>> Jochen
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>> Sorry, maybe my question was a but unclear.
>>>>>>>>>> Do you have finite cut-off lengths, or do you have pbc=no and
>>>>>>>>>> cut-off's
>>>>>>>>>> set to 0 (infinity).
>>>>>>>>>>
>>>>>>>>>> Berk
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>>> Berk
>>>>>>>>>>>>
>>>>>>>>>>>> Jochen Hub wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>> Hi Berk,
>>>>>>>>>>>>>
>>>>>>>>>>>>> yes, I have always reconfigured with distclean and
>>>>>>>>>>>>> everything.
>>>>>>>>>>>>> And
>>>>>>>>>>>>> checked that no CC variables or similar were messing up
>>>>>>>>>>>>> something. I
>>>>>>>>>>>>> could well imagine that the problem is again due to virtual
>>>>>>>>>>>>> sites
>>>>>>>>>>>>> which I have in my structure.
>>>>>>>>>>>>>
>>>>>>>>>>>>> In addition, I am getting LINCS warnings during EM with
>>>>>>>>>>>>> the 405
>>>>>>>>>>>>> from
>>>>>>>>>>>>> a
>>>>>>>>>>>>> few weeks ago, but *not* related to the bug you fixed
>>>>>>>>>>>>> recently
>>>>>>>>>>>>> (with
>>>>>>>>>>>>> CGs with only vsites). These lincs warnings appear
>>>>>>>>>>>>> typically in
>>>>>>>>>>>>> lysines, somewhere between the last carbon and the NH3 in the
>>>>>>>>>>>>> lysine
>>>>>>>>>>>>> chain. Noteworthy, the warnings did not appear with steepest
>>>>>>>>>>>>> descent,
>>>>>>>>>>>>> but with conjugate gradient. Higher lincs-order did not
>>>>>>>>>>>>> help, but
>>>>>>>>>>>>> even
>>>>>>>>>>>>> increased the large changes in angles. For example:
>>>>>>>>>>>>>
>>>>>>>>>>>>> atom 1 atom 2 angle previous, current, constraint length
>>>>>>>>>>>>> 886 889 34.3 0.1583 0.1582 0.1583
>>>>>>>>>>>>> 886 890 33.8 0.1583 0.1580 0.1583
>>>>>>>>>>>>> 889 890 34.0 0.0802 0.0805 0.0802
>>>>>>>>>>>>> 1291 1294 33.8 0.1583 0.1578 0.1583
>>>>>>>>>>>>> 1291 1295 34.3 0.1583 0.1586 0.1583
>>>>>>>>>>>>> 1294 1295 32.3 0.0802 0.0803 0.0802
>>>>>>>>>>>>>
>>>>>>>>>>>>> where the respective atoms are:
>>>>>>>>>>>>> 886 amber99_11 55 LYP CE 822 -0.0143
>>>>>>>>>>>>> 14.026
>>>>>>>>>>>>> ;
>>>>>>>>>>>>> qtot -3.006
>>>>>>>>>>>>> 887 amber99_28 55 LYP HE1 823
>>>>>>>>>>>>> 0.1135 0
>>>>>>>>>>>>> ;
>>>>>>>>>>>>> qtot -2.893
>>>>>>>>>>>>> 888 amber99_28 55 LYP HE2 824
>>>>>>>>>>>>> 0.1135 0
>>>>>>>>>>>>> ;
>>>>>>>>>>>>> qtot -2.779
>>>>>>>>>>>>> 889 MNH3 55 LYP MNZ1 825 0
>>>>>>>>>>>>> 8.517
>>>>>>>>>>>>> ;
>>>>>>>>>>>>> qtot -2.779
>>>>>>>>>>>>> 890 MNH3 55 LYP MNZ2 825 0
>>>>>>>>>>>>> 8.517
>>>>>>>>>>>>> ;
>>>>>>>>>>>>> qtot -2.779
>>>>>>>>>>>>> 891 amber99_39 55 LYP NZ 825
>>>>>>>>>>>>> -0.3854 0
>>>>>>>>>>>>> ;
>>>>>>>>>>>>> qtot -3.165
>>>>>>>>>>>>> 892 amber99_17 55 LYP HZ1 826
>>>>>>>>>>>>> 0.34 0
>>>>>>>>>>>>> ;
>>>>>>>>>>>>> qtot -2.825
>>>>>>>>>>>>> 893 amber99_17 55 LYP HZ2 827
>>>>>>>>>>>>> 0.34 0
>>>>>>>>>>>>> ;
>>>>>>>>>>>>> qtot -2.485
>>>>>>>>>>>>> 894 amber99_17 55 LYP HZ3 828
>>>>>>>>>>>>> 0.34 0
>>>>>>>>>>>>> ;
>>>>>>>>>>>>> qtot -2.145
>>>>>>>>>>>>>
>>>>>>>>>>>>> The atoms around nr 1291 are also the tip of a lysine side
>>>>>>>>>>>>> chain.
>>>>>>>>>>>>> 1291 amber99_11 80 LYP CE 1189 -0.0143
>>>>>>>>>>>>> 14.026
>>>>>>>>>>>>> ;
>>>>>>>>>>>>> qtot -4.006
>>>>>>>>>>>>> 1292 amber99_28 80 LYP HE1 1190
>>>>>>>>>>>>> 0.1135 0
>>>>>>>>>>>>> ;
>>>>>>>>>>>>> qtot -3.893
>>>>>>>>>>>>> 1293 amber99_28 80 LYP HE2 1191
>>>>>>>>>>>>> 0.1135 0
>>>>>>>>>>>>> ;
>>>>>>>>>>>>> qtot -3.779
>>>>>>>>>>>>> 1294 MNH3 80 LYP MNZ1 1192 0
>>>>>>>>>>>>> 8.517
>>>>>>>>>>>>> ;
>>>>>>>>>>>>> qtot -3.779
>>>>>>>>>>>>> 1295 MNH3 80 LYP MNZ2 1192 0
>>>>>>>>>>>>> 8.517
>>>>>>>>>>>>> ;
>>>>>>>>>>>>> qtot -3.779
>>>>>>>>>>>>> 1296 amber99_39 80 LYP NZ 1192
>>>>>>>>>>>>> -0.3854 0
>>>>>>>>>>>>> ;
>>>>>>>>>>>>> qtot -4.165
>>>>>>>>>>>>> 1297 amber99_17 80 LYP HZ1 1193
>>>>>>>>>>>>> 0.34 0
>>>>>>>>>>>>> ;
>>>>>>>>>>>>> qtot -3.825
>>>>>>>>>>>>> 1298 amber99_17 80 LYP HZ2 1194
>>>>>>>>>>>>> 0.34 0
>>>>>>>>>>>>> ;
>>>>>>>>>>>>> qtot -3.485
>>>>>>>>>>>>> 1299 amber99_17 80 LYP HZ3 1195
>>>>>>>>>>>>> 0.34 0
>>>>>>>>>>>>> ;
>>>>>>>>>>>>> qtot -3.145
>>>>>>>>>>>>>
>>>>>>>>>>>>> Jochne
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> Berk Hess wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>> 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:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> 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:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> 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:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> 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
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>> gmx-developers mailing list
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>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>> gmx-developers mailing list
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>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>> _______________________________________________
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>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> ---------------------------------------------------
>>>>>>>>> Dr. Jochen Hub
>>>>>>>>> Molecular Biophysics group
>>>>>>>>> Dept. of Cell & Molecular Biology
>>>>>>>>> Uppsala University. Box 596, 75124 Uppsala, Sweden.
>>>>>>>>> Phone: +46-18-4714451 Fax: +46-18-511755
>>>>>>>>> ---------------------------------------------------
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> gmx-developers mailing list
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>>>>>>>>>
>>>>>>>>>
>>>>>>>> _______________________________________________
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>>>>>>>
>>>>>> _______________________________________________
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>>>>>
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>
--
---------------------------------------------------
Dr. Jochen Hub
Molecular Biophysics group
Dept. of Cell & Molecular Biology
Uppsala University. Box 596, 75124 Uppsala, Sweden.
Phone: +46-18-4714451 Fax: +46-18-511755
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