[gmx-developers] QMMM, exclusions and neighbor search
Gerrit Groenhof
ggroenh at gwdg.de
Mon Mar 8 13:23:09 CET 2010
hess at sbc.su.se wrote:
> Ah, wait, but what happens to the LJ interactions?
> These will also be excluded. How is LJ treated
> between qm atoms?
>
Absent. There should be no LJ. THis is why the QM exclusions are
generated. Charges are simply set to zero.
Gerrit
> Berk
>
>
>> Hi,
>>
>> I think that we need two warnings in grompp when you have multiple
>> molecule types with qm atoms.
>> One when you do not use energygroup exclusions
>> and a second want even if you do, but you use PME.
>>
>> Berk
>>
>>
>>> hess at sbc.su.se wrote:
>>>
>>>> Hi,
>>>>
>>>> Gerrit, are you sure?
>>>> Did 3.3 really not add exclusions between qm atoms in different
>>>> molecules?
>>>>
>>>>
>>> It did. Maybe I did not make that clear. I had not realized this problem
>>> in 4 onward, because I always use one topology file. Even water I
>>> include explicitly.
>>>
>>>
>>>> Anyhow, with PME this still would not be correct.
>>>> The PME exclusion forces are determined as erf(beta*r)/r,
>>>> which is accurate at short distance, but quite wrong at a distance
>>>> of half the box length.
>>>>
>>>>
>>> In QM/MM the Coulomb expression is used. Therefore, the use of ewald is
>>> not recommended and I still use cutoff. The ONIOM based QM/MM, all
>>> interactions between the subsystems are evaluated at the MM level, so
>>> Ewald can be used.
>>>
>>>
>>>> Only doing an extra mesh calculation would fix this.
>>>> I am currently considering if that would be worth implementing.
>>>>
>>> The long range interaction between the QM subsystems in different boxes
>>> can be effectively done by using partial charges on the QM atoms and
>>> evaluating these interactions in the MM part. The charges can be fitted
>>> after the wavefuntion has been evaluated. However, what is missing is
>>> then the effect of the periodic images on the computations of the QM
>>> energy and charges. I have not found a satisfactory solution for this,
>>> although they must be out there already.
>>>
>>>> Berk
>>>>
>>>>
>>>>
>>>>> Hi Pia,
>>>>>
>>>>> It has indeed always been like this. Therefore, the fix of incuding
>>>>> the
>>>>> QM atoms in the energy group exclusions will have the same effect as
>>>>> explicitly removing the interactions.
>>>>>
>>>>>
>>>>> Gerrit
>>>>>
>>>>>
>>>>> Pia Toelle wrote:
>>>>>
>>>>>
>>>>>> Hi Berk.
>>>>>>
>>>>>> It just came to my mind, that there are already some QM-QM
>>>>>> interactions
>>>>>> excluded in the code. (My first remark in July 2009 was, that ONLY
>>>>>> the
>>>>>> nonbonded interaction of QM atoms belonging to the SAME molecule
>>>>>> (Gromacs 4.x.x).)
>>>>>>
>>>>>> So what about the "original" Gromacs 4.0.5 code and the use of QM/MM
>>>>>> and
>>>>>> PME? And the Gromacs 3.x.x code where QM-nonbonded interaction has
>>>>>> also
>>>>>> been excluded as far as I remember.
>>>>>>
>>>>>> Pia
>>>>>>
>>>>>>
>>>>>> Pia Toelle wrote:
>>>>>>
>>>>>>
>>>>>>
>>>>>>> Hi.
>>>>>>>
>>>>>>> So what's about my idea just to set the QM-QM interaction in
>>>>>>> "sys->ffparams" (in topio.c) to zero by including special
>>>>>>> QM-atomtypes.
>>>>>>> Do you see any problem there? For me it seems to work.
>>>>>>>
>>>>>>> Pia
>>>>>>>
>>>>>>>
>>>>>>> Berk Hess wrote:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>> Hi,
>>>>>>>>
>>>>>>>> With PME you can not easily exclude Coulomb interactions between
>>>>>>>> atom
>>>>>>>> pairs that come from
>>>>>>>> the PME mesh part. You would need one or multiple (I don't recall
>>>>>>>> now)
>>>>>>>> extra mesh calculations
>>>>>>>> to do that. It can be done, but requires some coding effort.
>>>>>>>>
>>>>>>>> Berk
>>>>>>>>
>>>>>>>> Pia Toelle wrote:
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>> Hello.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Actually, we are using PME (and our QM-calculation also uses pbc
>>>>>>>>> with
>>>>>>>>> Ewald summation). What problem do you refer to?
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Best wishes,
>>>>>>>>> Pia
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Berk Hess wrote:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> Hi,
>>>>>>>>>>
>>>>>>>>>> I suggested a simple solution for this problem to Gerrit, which
>>>>>>>>>> does
>>>>>>>>>> not
>>>>>>>>>> require code changes,
>>>>>>>>>> except for a check in grompp.
>>>>>>>>>>
>>>>>>>>>> I think you can simply use energy group exclusions by putting all
>>>>>>>>>> the qm
>>>>>>>>>> atoms in a separate
>>>>>>>>>> energy group and using: energygrp_excl = qm qm
>>>>>>>>>> This should do what you want, except when using PME and to a
>>>>>>>>>> certain
>>>>>>>>>> extent also reaction field.
>>>>>>>>>> But for those methods it is quite complicated to come up with a
>>>>>>>>>> proper
>>>>>>>>>> scheme.
>>>>>>>>>>
>>>>>>>>>> Berk
>>>>>>>>>>
>>>>>>>>>> Pia Toelle wrote:
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> Hi Gerrit.
>>>>>>>>>>>
>>>>>>>>>>> I made the following changes in src/kernel/topio.c:
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> - "generate_qmexcl": "molblock" filling changed (I am not sure,
>>>>>>>>>>> if
>>>>>>>>>>> this
>>>>>>>>>>> was related to the QM-QM interaction problem)
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> - added "generate_qm_atom_type": new QM-atomtype for all
>>>>>>>>>>> atomtypes
>>>>>>>>>>> added
>>>>>>>>>>> ( sys->atomtypes.nr were doubled)
>>>>>>>>>>> The added QM-atomtypes have zeros in sys->ffparams for the QM-QM
>>>>>>>>>>> non-bonded interaction.
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> I hope, that the changes in the attached file topio.c are
>>>>>>>>>>> understandable
>>>>>>>>>>> and that it will help you.
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Greetings,
>>>>>>>>>>> Pia
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Gerrit Groenhof wrote:
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>> Hallo Pia,
>>>>>>>>>>>>
>>>>>>>>>>>> Sorry for not getting back on this issue earlier.
>>>>>>>>>>>>
>>>>>>>>>>>> Have you been able to fix this bug?
>>>>>>>>>>>>
>>>>>>>>>>>> BEst wishes,
>>>>>>>>>>>>
>>>>>>>>>>>> Gerrit
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> On 11 Aug 2009, at 13:10, Pia Toelle wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>> Okay.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Thanks for your reply. I will try to do so.
>>>>>>>>>>>>> Please, tell me if their are any news concerning this problem.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Cheers,
>>>>>>>>>>>>> Pia
>>>>>>>>>>>>>
>>>>>>>>>>>>> Berk Hess wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> That would work.
>>>>>>>>>>>>>> But we should certainly fix the code.
>>>>>>>>>>>>>> I did not think of this situation when introducing the
>>>>>>>>>>>>>> moltype
>>>>>>>>>>>>>> data
>>>>>>>>>>>>>> structure in version 4.0.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Berk
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Pia Toelle wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Hello.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> To avoid a different handling of QM-atoms of different
>>>>>>>>>>>>>>> molecule
>>>>>>>>>>>>>>> types,
>>>>>>>>>>>>>>> would it be possible to put all QM atoms in one molblock and
>>>>>>>>>>>>>>> moltype, as
>>>>>>>>>>>>>>> the molblocks ans moltypes are filled and defined anyway in
>>>>>>>>>>>>>>> generate_qmexcl? Or would this influence other parts of the
>>>>>>>>>>>>>>> program?
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> greetings
>>>>>>>>>>>>>>> Pia
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Gerrit Groenhof wrote:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> I had not realized your previous question had not been
>>>>>>>>>>>>>>>> answered
>>>>>>>>>>>>>>>> completely, sorry.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> In 3.3 it was a bit more intuitive, also for me.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> In the generate_qmexcl there is a loop over all molblocks.
>>>>>>>>>>>>>>>> Thus all qm
>>>>>>>>>>>>>>>> atoms are found, even if they are in different molecules.
>>>>>>>>>>>>>>>> However, you
>>>>>>>>>>>>>>>> might have a point that between molecules the qm atoms do
>>>>>>>>>>>>>>>> not
>>>>>>>>>>>>>>>> seem to
>>>>>>>>>>>>>>>> get excluded. Such situation could happen, for example if
>>>>>>>>>>>>>>>> part
>>>>>>>>>>>>>>>> of the
>>>>>>>>>>>>>>>> protein and a few waters are treated at the QM level, which
>>>>>>>>>>>>>>>> is
>>>>>>>>>>>>>>>> typical
>>>>>>>>>>>>>>>> for enzymes. To avoid problems (if any), you can include
>>>>>>>>>>>>>>>> such
>>>>>>>>>>>>>>>> waters in
>>>>>>>>>>>>>>>> the .itp file of the protein. But it should work also with
>>>>>>>>>>>>>>>> the
>>>>>>>>>>>>>>>> different QM atom in different topologies and I will look
>>>>>>>>>>>>>>>> into this .
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Gerrit
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> On 10 Aug 2009, at 18:27, Pia Toelle wrote:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Hello.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> I still have problems with "generate_qmexcl" in version
>>>>>>>>>>>>>>>>> 4.0.5.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Comparing to earlier version 3.3.3, one notices that the
>>>>>>>>>>>>>>>>> data
>>>>>>>>>>>>>>>>> structure
>>>>>>>>>>>>>>>>> moltype and molblock are included. In the earlier version,
>>>>>>>>>>>>>>>>> qm
>>>>>>>>>>>>>>>>> exclusions
>>>>>>>>>>>>>>>>> were generated for each QM-atom inside the system, now in
>>>>>>>>>>>>>>>>> version 4.0.5,
>>>>>>>>>>>>>>>>> they are generated per atom inside each molecule type.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> I still wounder whether the exclusions between QM-atoms of
>>>>>>>>>>>>>>>>> different
>>>>>>>>>>>>>>>>> molecule types are considered here and - if yes - how. Or
>>>>>>>>>>>>>>>>> -
>>>>>>>>>>>>>>>>> if not -
>>>>>>>>>>>>>>>>> where this is done.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Is the splitting of the QM part into molblock's correct?
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> I would be glad for any comment or reply! Please tell me
>>>>>>>>>>>>>>>>> if
>>>>>>>>>>>>>>>>> my question
>>>>>>>>>>>>>>>>> is not precise.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Pia
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Pia Toelle wrote:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Hello Gerrit.
>>>>>>>>>>>>>>>>>> Thanks for the reply, it helped a lot, but I still have
>>>>>>>>>>>>>>>>>> some
>>>>>>>>>>>>>>>>>> problems to
>>>>>>>>>>>>>>>>>> understand.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> As far as I understood in "generate_qmexcl" the QM
>>>>>>>>>>>>>>>>>> molecules
>>>>>>>>>>>>>>>>>> are put
>>>>>>>>>>>>>>>>>> into separate molblock and each molecule has its own
>>>>>>>>>>>>>>>>>> moleculetype.
>>>>>>>>>>>>>>>>>> Then "generate_qmexcl_moltype" is called and the
>>>>>>>>>>>>>>>>>> exclusions
>>>>>>>>>>>>>>>>>> are set.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> At first an array "qm_arr" is generated. As the loop
>>>>>>>>>>>>>>>>>> "for(i=0;i<molt->atoms.nr;i++)" only passes through the
>>>>>>>>>>>>>>>>>> atoms with the
>>>>>>>>>>>>>>>>>> same moleculetype.
>>>>>>>>>>>>>>>>>> "sys->moltype[--].excls" contains the exclusions between
>>>>>>>>>>>>>>>>>> Atoms of the
>>>>>>>>>>>>>>>>>> same topologie.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Are the nonbonded interactions listed in the ilist and
>>>>>>>>>>>>>>>>>> excluded by
>>>>>>>>>>>>>>>>>> deleting them in this list?
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Where is the ilist generated in first place?
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Please correct my estimates.
>>>>>>>>>>>>>>>>>> Cheers,
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Pia
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Gerrit Groenhof wrote:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> The QM - QM interactions, both Coulomb and van der Waals
>>>>>>>>>>>>>>>>>>> are explicitly
>>>>>>>>>>>>>>>>>>> exluded.
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> The code for this begins with the comment
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> /* creating the exclusion block for the QM atoms. Each
>>>>>>>>>>>>>>>>>>> QM
>>>>>>>>>>>>>>>>>>> atom has
>>>>>>>>>>>>>>>>>>> * as excluded elements all the other QMatoms (and
>>>>>>>>>>>>>>>>>>> itself).
>>>>>>>>>>>>>>>>>>> */
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> In generate_qmexcl_moltype (topio.c).
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Thus the exclusionlists are expanded with all QM- QM
>>>>>>>>>>>>>>>>>>> interactions.
>>>>>>>>>>>>>>>>>>> The coulomb interactions are handled a bit more dirty:
>>>>>>>>>>>>>>>>>>> In
>>>>>>>>>>>>>>>>>>> the
>>>>>>>>>>>>>>>>>>> initialisation (qmmm.c), these charges are put to zero.
>>>>>>>>>>>>>>>>>>> Thus the standard nbsearching will look at the
>>>>>>>>>>>>>>>>>>> exclusions
>>>>>>>>>>>>>>>>>>> and check
>>>>>>>>>>>>>>>>>>> if a
>>>>>>>>>>>>>>>>>>> particle is charged. This way it will never include the
>>>>>>>>>>>>>>>>>>> QM
>>>>>>>>>>>>>>>>>>> QM atom
>>>>>>>>>>>>>>>>>>> pairs, or QM MM coulomb interactions.
>>>>>>>>>>>>>>>>>>> The QMMM nbsearching in the next step takes the QM atoms
>>>>>>>>>>>>>>>>>>> as
>>>>>>>>>>>>>>>>>>> i-particles
>>>>>>>>>>>>>>>>>>> and searches all MM neighbours.
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Best wishes,
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Gerrit
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> On 15 Jul 2009, at 20:10, Pia Toelle wrote:
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Hello
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> (I am using Gromacs 4.0.5 (QM/MM))
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> I have a question about the exclusion of nonbonded
>>>>>>>>>>>>>>>>>>>> (specially VdW)
>>>>>>>>>>>>>>>>>>>> interaction in QM/MM simulation. The coulomb and VdW
>>>>>>>>>>>>>>>>>>>> interaction
>>>>>>>>>>>>>>>>>>>> between
>>>>>>>>>>>>>>>>>>>> two QM Atoms should not be calculated by Gromacs as the
>>>>>>>>>>>>>>>>>>>> QM-QM
>>>>>>>>>>>>>>>>>>>> interaction is done by the QM-program.
>>>>>>>>>>>>>>>>>>>> Where (and how) in the code is the VdW (and also
>>>>>>>>>>>>>>>>>>>> coulomb)
>>>>>>>>>>>>>>>>>>>> interaction
>>>>>>>>>>>>>>>>>>>> between two QM atoms excluded?
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Please also comment on the following:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> (topio.c called by grompp.c)
>>>>>>>>>>>>>>>>>>>> "generate_qmexcl" and "generate_qmexcl_moltype", here
>>>>>>>>>>>>>>>>>>>> the
>>>>>>>>>>>>>>>>>>>> exclusions for
>>>>>>>>>>>>>>>>>>>> the INTRA-molecular interaction are set. Is this right?
>>>>>>>>>>>>>>>>>>>> What is about
>>>>>>>>>>>>>>>>>>>> the Interaction between different QM-Molecules?
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> (ns.c)
>>>>>>>>>>>>>>>>>>>> In "search_neighbours" the "nsgrid_core" is called to
>>>>>>>>>>>>>>>>>>>> set
>>>>>>>>>>>>>>>>>>>> up the
>>>>>>>>>>>>>>>>>>>> neighbor lists (for all atoms QM and MM !?), then it is
>>>>>>>>>>>>>>>>>>>> called to
>>>>>>>>>>>>>>>>>>>> set up
>>>>>>>>>>>>>>>>>>>> the QM/MM neighbor list.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> (force.c)
>>>>>>>>>>>>>>>>>>>> In "do_forces" the "do_force_lowlevel" is called, there
>>>>>>>>>>>>>>>>>>>> the
>>>>>>>>>>>>>>>>>>>> QM-calculation and "do_nonbonded" takes place. The
>>>>>>>>>>>>>>>>>>>> later
>>>>>>>>>>>>>>>>>>>> does not
>>>>>>>>>>>>>>>>>>>> contain any information about the atom being QM or not,
>>>>>>>>>>>>>>>>>>>> as
>>>>>>>>>>>>>>>>>>>> far as I
>>>>>>>>>>>>>>>>>>>> can
>>>>>>>>>>>>>>>>>>>> see. Therefore, I believe, that the decision to
>>>>>>>>>>>>>>>>>>>> calculate
>>>>>>>>>>>>>>>>>>>> VdW was made
>>>>>>>>>>>>>>>>>>>> by setting up the lists. Is this right???
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Thanks in advance,
>>>>>>>>>>>>>>>>>>>> Pia Tölle
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> BCCMS, university of Bremen, Germany
>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>> gmx-developers mailing list
>>>>>>>>>>>>>>>>>>>> gmx-developers at gromacs.org
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>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>>>> Gerrit Groenhof
>>>>>>>>>>>>>>>>>>> MPI biophysical chemistry
>>>>>>>>>>>>>>>>>>> Goettingen
>>>>>>>>>>>>>>>>>>> Germany
>>>>>>>>>>>>>>>>>>> http://wwwuser.gwdg.de/~ggroenh/
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>> gmx-developers mailing list
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>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>> gmx-developers mailing list
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>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>> gmx-developers mailing list
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>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>> Gerrit Groenhof
>>>>>>>>>>>>>>>> MPI biophysical chemistry
>>>>>>>>>>>>>>>> Goettingen
>>>>>>>>>>>>>>>> Germany
>>>>>>>>>>>>>>>> http://wwwuser.gwdg.de/~ggroenh/
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>> gmx-developers mailing list
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>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>> gmx-developers mailing list
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>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>> gmx-developers mailing list
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>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>> gmx-developers mailing list
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>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>> --
>>>>>>>>>>>> Gerrit Groenhof
>>>>>>>>>>>> MPI biophysical chemistry
>>>>>>>>>>>> Goettingen
>>>>>>>>>>>> Germany
>>>>>>>>>>>> http://wwwuser.gwdg.de/~ggroenh/
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>
>>>>> --
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>>>>
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