[gmx-developers] Segfault during EM in recent git version
Jochen Hub
jochen at xray.bmc.uu.se
Tue Oct 6 17:03:38 CEST 2009
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
>>>>>>>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-developers
>>>>>>>>>>>>> Please don't post (un)subscribe requests to the list. Use the
>>>>>>>>>>>>> www
>>>>>>>>>>>>> interface or send it to gmx-developers-request at gromacs.org.
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> 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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