[gmx-developers] Segfault during EM in recent git version
David van der Spoel
spoel at xray.bmc.uu.se
Wed Oct 7 11:57:26 CEST 2009
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?
>
> 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
>>>>>>>>>>>>>>> gmx-developers at gromacs.org
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>>>>>>>>>>>>>>> the
>>>>>>>>>>>>>>> www
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>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>> gmx-developers mailing list
>>>>>>>>>>>>> gmx-developers at gromacs.org
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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
>>>>>>>> ---------------------------------------------------
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> gmx-developers mailing list
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>>>>>>>>
>>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> gmx-developers mailing list
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>>>>>>>
>>>>>>
>>>>> _______________________________________________
>>>>> gmx-developers mailing list
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>>>>
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--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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