[gmx-users] Re: Carbon Nanotube Simulation Issues

Robert Johnson bobjohnson1981 at gmail.com
Sat Jul 28 00:03:40 CEST 2007


You could probably dispense with the dihedral terms (as long as you
aren't interested in the mechanical properties of the CNT), but I
would at least include a bond and angle term for the nanotube atoms.


On 7/27/07, Yang Ye <leafyoung at yahoo.com> wrote:
> On one hand, use -pp for grompp for whatever warnings, so you may what's
> on the line which causes problems.
> On the other hand, find force field parameters for carbon nanotubes. For
> a simple rigid nanotube, I reckon that you may only need bond potential
> for every bond.
>
> On 7/27/2007 10:42 PM, Christopher Stiles wrote:
> > They are in the ffgmx.itp file and maybe I missed it but I didn't read about
> > people having to change it for CNT's, but maybe so I will look further into
> > this and try some things... I will let you guys know where I get. Also if
> > any one knows already knows please feel free to give me a hint or ref.
> >
> > Thanks so much,
> >
> > ~Christopher Stiles
> > College of Nanoscale Science and Engineering (CNSE)
> > State University of New York, Albany, New York 12203, USA
> >
> >
> >> -----Original Message-----
> >> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> >> On Behalf Of Robert Johnson
> >> Sent: Friday, July 27, 2007 10:28 AM
> >> To: Discussion list for GROMACS users
> >> Subject: Re: [gmx-users] Re: Carbon Nanotube Simulation Issues
> >>
> >> Did you define angle and dihedral parameters in the [ angletypes ] and
> >> [ dihedraltypes ] sections of your .itp file?
> >> Bob
> >>
> >> On 7/27/07, Christopher Stiles <CS145331 at albany.edu> wrote:
> >>
> >>> The warnings are:
> >>> ...
> >>> WARNING 701 [file "SWNT_6_6_144.top", line 1278]:
> >>>   No default Angle types, using zeroes
> >>> WARNING 702 [file "SWNT_6_6_144.top", line 1278]:
> >>>   No default Angle types for perturbed atoms, using normal values
> >>> ...
> >>> WARNING 793 [file "SWNT_6_6_144.top", line 1327]:
> >>>   No default Proper Dih. types, using zeroes
> >>> WARNING 794 [file "SWNT_6_6_144.top", line 1327]:
> >>>   No default Proper Dih. types for perturbed atoms, using normal values
> >>> ...
> >>> Those are the 2 errors, here is a link to the full output:
> >>> http://cs86.com/CNSE/files/Grompp_Output.txt
> >>>
> >>> Thank you again,
> >>>
> >>> ~Christopher Stiles
> >>> College of Nanoscale Science and Engineering (CNSE)
> >>> State University of New York, Albany, New York 12203, USA
> >>>
> >>>
> >>>
> >>>> -----Original Message-----
> >>>> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> >>>>
> >> bounces at gromacs.org]
> >>
> >>>> On Behalf Of Yang Ye
> >>>> Sent: Friday, July 27, 2007 4:45 AM
> >>>> To: Discussion list for GROMACS users
> >>>> Subject: Re: [gmx-users] Re: Carbon Nanotube Simulation Issues
> >>>>
> >>>> On 7/27/2007 4:53 AM, Christopher Stiles wrote:
> >>>>
> >>>>> Ok here is the update:
> >>>>> I have made the following changes:
> >>>>> I almost doubled my box size and limited the saturation to 256 water
> >>>>> molecules.
> >>>>> I removed the include from my *.mdp file
> >>>>> Changed the includes in my topology file to:
> >>>>> #include "ffgmx.itp"
> >>>>> #include "spc.itp"
> >>>>> And added the following line of code to the [ bondtype ] section of
> >>>>>
> >> the
> >>
> >>>>> ffgmxbon.itp file:
> >>>>> C    C    1   0.14210     478900.
> >>>>>
> >>>>> I use the files in this zip file to run grompp:
> >>>>>
> >>>>> http://cs86.com/CNSE/SWNT.zip
> >>>>>
> >>>>> running grompp I use the following command:
> >>>>> grompp -f mdout_test.mdp -c SWNT_6_6_144_b4em.gro -p SWNT_6_6_144.top
> >>>>> -maxwarn 10000 -pp
> >>>>>
> >>>>>
> >>>> What's the warnings?
> >>>>
> >>>>> It works but there is 1176 warnings, which I am assuming this is a
> >>>>>
> >>>> problem?
> >>>>
> >>>>> Then I run mdrun using the following command:
> >>>>> Mdrun -s topol.tpr
> >>>>> It works just fine
> >>>>> Then I can view it with ngmx using the following command:
> >>>>> ngmx -f traj.xtc -s topol.tpr.
> >>>>> This works just fine as well.
> >>>>>
> >>>>> My question is are the warnings ok/normal or is there some fix that
> >>>>>
> >> needs
> >>
> >>>> to
> >>>>
> >>>>> be made?
> >>>>>
> >>>>> Thank you again Yang, Bob, and every one else you have all been a
> >>>>>
> >> great
> >>
> >>>>> help!
> >>>>>
> >>>>> ~Christopher Stiles
> >>>>> College of Nanoscale Science and Engineering (CNSE)
> >>>>> State University of New York, Albany, New York 12203, USA
> >>>>>
> >>>>> ________________________________________________
> >>>>>
> >>>>>
> >>>>>
> >>>>>> You shall include ffgmx.itp only and make change to ffgmxbon.itp.
> >>>>>>
> >>>>>> On 7/27/2007 12:18 AM, Christopher Stiles wrote:
> >>>>>>
> >>>>>>
> >>>>>>> Yang & Bob,
> >>>>>>>
> >>>>>>> When I change the include to be ffgmxbon.itp instead of ffgmx.itp I
> >>>>>>>
> >> get
> >>
> >>>>>> the
> >>>>>>
> >>>>>>
> >>>>>>> following error:
> >>>>>>> ****************************
> >>>>>>> Fatal error:
> >>>>>>> Invalid order for directive bondtypes, file ""ffgmxbon.itp"", line 1
> >>>>>>> ****************************
> >>>>>>> I believe it is because when just including ffgmxbon.itp it never
> >>>>>>>
> >> calls
> >>
> >>>>>> up
> >>>>>>
> >>>>>>
> >>>>>>> ffgmxnb.itp so there for atomtypes are not defined first ect...
> >>>>>>> Although my understanding of this whole process is very limited...
> >>>>>>>
> >>>>>>> Thank you all very much for your patience and guidance helping me
> >>>>>>>
> >>>> along!
> >>>>
> >>>>>>> ~Christopher Stiles
> >>>>>>> College of Nanoscale Science and Engineering (CNSE)
> >>>>>>> State University of New York, Albany, New York 12203, USA
> >>>>>>>
> >>>>>>> ________________________________________________
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>> -----Original Message-----
> >>>>>>>> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> >>>>>>>>
> >>>>>>>>
> >>>>>> bounces at gromacs.org]
> >>>>>>
> >>>>>>
> >>>>>>>> On Behalf Of Yang Ye
> >>>>>>>> Sent: Thursday, July 26, 2007 11:34 AM
> >>>>>>>> To: Discussion list for GROMACS users
> >>>>>>>> Subject: Re: [gmx-users] Re: Carbon Nanotube Simulation Issues
> >>>>>>>>
> >>>>>>>> Hi,
> >>>>>>>>
> >>>>>>>> It's my typo again. Sorry. It shall be ffgmxbon.itp.
> >>>>>>>>
> >>>>>>>> On 7/26/2007 10:57 PM, Christopher Stiles wrote:
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>> Yang,
> >>>>>>>>>  Thank you again for being so detailed. I do have 2 questions
> >>>>>>>>>
> >>>> though,
> >>>>
> >>>>>>>>> when you say:
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>> So you shall change ffG43b1.itp to ffgmx.itp. And add the line
> >>>>>>>>>> C    C    1   0.14210     478900.
> >>>>>>>>>>
> >>>>>>>>>> To the end of section [ bondtypes ], not the end of the whole
> >>>>>>>>>>
> >> file.
> >>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>> You mean in the topology file I assume for the changing from
> >>>>>>>>>
> >>>>>>>>>
> >>>>>> ffG43b1.itp
> >>>>>>
> >>>>>>
> >>>>>>>> to
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>> ffgmx.itp. But the adding of the line is what I am having trouble
> >>>>>>>>>
> >>>> with,
> >>>>
> >>>>>>>>> should it go in the topology file or ffgmx.itp? because neither
> >>>>>>>>>
> >> have
> >>
> >>>> a
> >>>>
> >>>>>>>>> [ bondtypes ] section and when I add one it just gives me errors.
> >>>>>>>>>
> >>>> From
> >>>>
> >>>>>>>>>
> >>>>>>>> what
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>> I understand from the manual it is only the *.itp files that can
> >>>>>>>>>
> >> have
> >>
> >>>>>>>>>
> >>>>>>>> those
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>> sections, so I think maybe it should go in the ffgmx.itp file I am
> >>>>>>>>>
> >>>> just
> >>>>
> >>>>>>>>>
> >>>>>>>> not
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>> making the addition to the file properly.
> >>>>>>>>> Also here is a copy of the ffgmx.itp file:
> >>>>>>>>> ########################
> >>>>>>>>> #define _FF_GROMACS
> >>>>>>>>> #define _FF_GROMACS1
> >>>>>>>>>
> >>>>>>>>> [ defaults ]
> >>>>>>>>> ; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
> >>>>>>>>>   1             1               no              1.0     1.0
> >>>>>>>>>
> >>>>>>>>> #include "ffgmxnb.itp"
> >>>>>>>>> #include "ffgmxbon.itp"
> >>>>>>>>> ########################
> >>>>>>>>> And here is a copy of my ffG43b1.itp file:
> >>>>>>>>> ########################
> >>>>>>>>> #define _FF_GROMOS96
> >>>>>>>>> #define _FF_GROMOS43B1
> >>>>>>>>>
> >>>>>>>>> [ defaults ]
> >>>>>>>>> ; nbfunc comb-rule       gen-pairs       fudgeLJ fudgeQQ
> >>>>>>>>>   1              1               no              1.0     1.0
> >>>>>>>>>
> >>>>>>>>> #include "ffG43b1nb.itp"
> >>>>>>>>> #include "ffG43b1bon.itp"
> >>>>>>>>> ########################
> >>>>>>>>>
> >>>>>>>>> Last of all this question is to any one, how do I reply to a
> >>>>>>>>>
> >> specific
> >>
> >>>>>>>>> thread? I have searched around and I have had no luck.
> >>>>>>>>>
> >>>>>>>>> Thank you so much for all of your help!
> >>>>>>>>>
> >>>>>>>>> ~Christopher Stiles
> >>>>>>>>> College of Nanoscale Science and Engineering (CNSE)
> >>>>>>>>> State University of New York, Albany, New York 12203, USA
> >>>>>>>>>
> >>>>>>>>> _______________________________________________________
> >>>>>>>>>
> >>>>>>>>> Hi,
> >>>>>>>>>
> >>>>>>>>> I missed one dash in the front. So it should be
> >>>>>>>>>
> >>>>>>>>> include = -IffG43b1.n2t
> >>>>>>>>>
> >>>>>>>>> The problem you had was because of improper usage of include, for
> >>>>>>>>>
> >>>> every
> >>>>
> >>>>>>>>>
> >>>>>>>> item
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>> to be put in include=, you shall prefix -I in the front. Since you
> >>>>>>>>>
> >>>> have
> >>>>
> >>>>>>>>>
> >>>>>>>> not
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>> put it, cpp couldn't finish parsing the topology file, so your
> >>>>>>>>>
> >>>> topology
> >>>>
> >>>>>>>>> contains nothing.
> >>>>>>>>>
> >>>>>>>>> ffG43b1.n2t is not necessary for grompp.
> >>>>>>>>>
> >>>>>>>>> You shall include spc.itp in your topology file to include the
> >>>>>>>>>
> >>>> topology
> >>>>
> >>>>>>>>>
> >>>>>>>> for
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>> water. So your file header shall be like
> >>>>>>>>>
> >>>>>>>>> #include "ffG43b1.itp"
> >>>>>>>>> #include "spc.itp"
> >>>>>>>>>
> >>>>>>>>> Last and most important, the line you added to ffgmxbon.itp is
> >>>>>>>>>
> >>>> useless
> >>>>
> >>>>>>>>> because you are using GROMOS96 force field.
> >>>>>>>>>
> >>>>>>>>> So you shall change ffG43b1.itp to ffgmx.itp. And add the line
> >>>>>>>>> C    C    1   0.14210     478900.
> >>>>>>>>>
> >>>>>>>>> To the end of section [ bondtypes ], not the end of the whole
> >>>>>>>>>
> >> file.
> >>
> >>>>>>>>> So the command line without -maxwarn can work properly. Note that
> >>>>>>>>>
> >> you
> >>
> >>>>>>>>>
> >>>>>>>> shall
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>> not use -maxwarn in most cases.
> >>>>>>>>> grompp -f mdout_test.mdp -c SWNT_6_6_144_b4em.gro -p
> >>>>>>>>> SWNT_6_6_144_post_genbox.top -pp
> >>>>>>>>>
> >>>>>>>>> The suffix _s is just what I have specified for my build. You
> >>>>>>>>>
> >> don't
> >>
> >>>>>> need
> >>>>>>
> >>>>>>
> >>>>>>>> the
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>> same setting.
> >>>>>>>>>
> >>>>>>>>> Regards,
> >>>>>>>>> Yang Ye
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> On 7/25/2007 10:29 PM, Christopher Stiles wrote:
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>> Yang,
> >>>>>>>>>> Thank you very much for you help. I am sorry I did not think to
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>> package
> >>>>>>
> >>>>>>
> >>>>>>>> my
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>>> files and commands up I will do so by the end of the day. As to
> >>>>>>>>>>
> >> the
> >>
> >>>>>>>>>> ffG43b1.n2t it was to get x2top to work, it defines single and
> >>>>>>>>>>
> >>>> double
> >>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>> bonded
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>> carbon so that I do not have to cap my tube with hydrogen.
> >>>>>>>>>>
> >> Although
> >>
> >>>> I
> >>>>
> >>>>>> am
> >>>>>>
> >>>>>>
> >>>>>>>>> not
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>> sure how you got the include to work with:
> >>>>>>>>>> include = IffG43b1.n2t
> >>>>>>>>>> Do you have a file named IffG43b1.n2t in your lib or your working
> >>>>>>>>>>
> >>>> dir?
> >>>>
> >>>>>>>>>> The file comes from the ffgmx.n2t file in the Gromacs lib but the
> >>>>>>>>>>
> >>>> name
> >>>>
> >>>>>>>>>>
> >>>>>>>> is
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>>> changes to ffG43b1.n2t and the following 2 lines are added:
> >>>>>>>>>> C       C       1       C                         ; CNT Carbon
> >>>>>>>>>>
> >> with
> >>
> >>>>>> one
> >>>>>>
> >>>>>>
> >>>>>>>>> bond
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>> C       C       2       C       C                ; CNT double
> >>>>>>>>>>
> >> bonded
> >>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>> Carbon
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>> Next must I use grompp_s? (I believe this is grompp with single
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>> accuracy,
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>>> correct?) Because if so I will have to compile it.
> >>>>>>>>>> Last question, by it gives a pass do you mean you get a little
> >>>>>>>>>>
> >> over
> >>
> >>>>>> 1500
> >>>>>>
> >>>>>>
> >>>>>>>>>> warnings and then get the following:
> >>>>>>>>>> Fatal error:
> >>>>>>>>>> No such moleculetype SOL
> >>>>>>>>>>
> >>>>>>>>>> Thank you so much for your help I really appreciate it,
> >>>>>>>>>>
> >>>>>>>>>> ~Christopher Stiles
> >>>>>>>>>> College of Nanoscale Science and Engineering (CNSE)
> >>>>>>>>>> State University of New York, Albany, New York 12203, USA
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>> Hi,
> >>>>>>>>>>>
> >>>>>>>>>>> Sorry that most of us on the list were too busy to read one full
> >>>>>>>>>>>
> >>>> page
> >>>>
> >>>>>>>>>>>
> >>>>>>>> of
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>>>> details and download individual files. We might just prefer to
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>> download
> >>>>>>
> >>>>>>
> >>>>>>>>>>> one package, and run a script file for us quickly dive into the
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>> problem.
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>>>> Is include in mdout_test.mdp a standard option? Where did you
> >>>>>>>>>>>
> >> get
> >>
> >>>> it?
> >>>>
> >>>>>> I
> >>>>>>
> >>>>>>
> >>>>>>>>>>> changed it to
> >>>>>>>>>>>
> >>>>>>>>>>> include = IffG43b1.n2t
> >>>>>>>>>>>
> >>>>>>>>>>> It works. Otherwise, cpp terminates before it generates a full
> >>>>>>>>>>>
> >> top.
> >>
> >>>>>>>>>>> grompp -pp is always a good friend for grompp error (and
> >>>>>>>>>>>
> >> thorough
> >>
> >>>>>>>>>>> reading of chapter 5 of manual).
> >>>>>>>>>>>
> >>>>>>>>>>> Next issue comes the format of ffG43b1.n2t. I don't think it
> >>>>>>>>>>>
> >>>> conforms
> >>>>
> >>>>>>>>>>>
> >>>>>>>> to
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>>>> any GROMACS topology format. Again where does it comes from?
> >>>>>>>>>>>
> >>>>>>>>>>> My grompp command line:
> >>>>>>>>>>> grompp_s -f mdout_test.mdp -c SWNT_6_6_144_b4em.gro -p
> >>>>>>>>>>> SWNT_6_6_144_post_genbox.top -maxwarn 10000000 -pp
> >>>>>>>>>>>
> >>>>>>>>>>> It gives a pass, at least.
> >>>>>>>>>>>
> >>>>>>>>>>> Hope you can work further on.
> >>>>>>>>>>>
> >>>>>>>>>>> Regards,
> >>>>>>>>>>> Yang Ye
> >>>>>>>>>>>
> >>>>>>>>>>> On 7/25/2007 2:41 AM, Christopher Stiles wrote:
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>>> I am trying to simulate a single wall carbon nanotube in a box
> >>>>>>>>>>>> solvated in water, at 300k for about 200ps. Also once I
> >>>>>>>>>>>>
> >> accomplish
> >>
> >>>>>>>>>>>> this I wish to fix either one end of the tube or fix the center
> >>>>>>>>>>>>
> >> of
> >>
> >>>>>>>>>>>> mass position, although this part is unimportant if I can not
> >>>>>>>>>>>>
> >> get
> >>
> >>>>>> the
> >>>>>>
> >>>>>>
> >>>>>>>>>>>> thing to run at all yet.
> >>>>>>>>>>>>
> >>>>>>>>>>>> I have created a page with a full detailed account of what I
> >>>>>>>>>>>>
> >> have
> >>
> >>>>>> done
> >>>>>>
> >>>>>>
> >>>>>>>>>>>> and tried so far. http://cs86.com/CNSE/SWNT.htm
> >>>>>>>>>>>>
> >>>>>>>>>>>> Please note all files where created with Vim in the unix
> >>>>>>>>>>>>
> >>>> environment
> >>>>
> >>>>>>>>>>>> so I think I have eliminated the formatting issues.
> >>>>>>>>>>>>
> >>>>>>>>>>>> Also that I have tried the simulation with many different sized
> >>>>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>> tubes
> >>>>>>
> >>>>>>
> >>>>>>>>>>>> from TubeGen
> >>>>>>>>>>>>
> >>>> (http://turin.nss.udel.edu/research/tubegenonline.html
> >>>>
> >>>>>> ),
> >>>>>>
> >>>>>>
> >>>>>>>>>>>> both with and without hydrogen capped ends (this is something I
> >>>>>>>>>>>>
> >>>> have
> >>>>
> >>>>>>>>>>>> read in the archives as a possible solution, it makes no
> >>>>>>>>>>>>
> >>>> difference
> >>>>
> >>>>>> in
> >>>>>>
> >>>>>>
> >>>>>>>>>>>> the end).
> >>>>>>>>>>>>
> >>>>>>>>>>>> I have come to the conclusion through the help of many of you
> >>>>>>>>>>>>
> >> that
> >>
> >>>>>> the
> >>>>>>
> >>>>>>
> >>>>>>>>>>>> *.pdb file from TubeGen and mainly the residue  UNK  among
> >>>>>>>>>>>>
> >> other
> >>
> >>>>>>>>>>>> things. If any one has had luck with using a TubeGen file to
> >>>>>>>>>>>>
> >>>> create
> >>>>
> >>>>>> a
> >>>>>>
> >>>>>>
> >>>>>>>>>>>> simulation please let me know as to how. Other wise I am
> >>>>>>>>>>>>
> >> looking
> >>
> >>>> at
> >>>>
> >>>>>> a
> >>>>>>
> >>>>>>
> >>>>>>>>>>>> few new options basically all of them involve writing my own
> >>>>>>>>>>>>
> >>>> files.
> >>>>
> >>>>>>>>>>>> I guess I am looking for advice where to go from here.
> >>>>>>>>>>>>
> >>>>>>>>>>>> ~Christopher Stiles
> >>>>>>>>>>>> College of Nanoscale Science and Engineering (CNSE)
> >>>>>>>>>>>> State University of New York, Albany, New York 12203, USA
> >>>>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>> _______________________________________________
> >>>>>>>>>> gmx-users mailing list    gmx-users at gromacs.org
> >>>>>>>>>> http://www.gromacs.org/mailman/listinfo/gmx-users
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> >>>>>>>>>>
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> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>> ------------------------------
> >>>>>>>>>
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> >>>>>
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> >>>>
> >>> _______________________________________________
> >>> gmx-users mailing list    gmx-users at gromacs.org
> >>> http://www.gromacs.org/mailman/listinfo/gmx-users
> >>> Please search the archive at http://www.gromacs.org/search before
> >>>
> >> posting!
> >>
> >>> Please don't post (un)subscribe requests to the list. Use the
> >>> www interface or send it to gmx-users-request at gromacs.org.
> >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >>>
> >>>
> >> _______________________________________________
> >> gmx-users mailing list    gmx-users at gromacs.org
> >> http://www.gromacs.org/mailman/listinfo/gmx-users
> >> Please search the archive at http://www.gromacs.org/search before posting!
> >> Please don't post (un)subscribe requests to the list. Use the
> >> www interface or send it to gmx-users-request at gromacs.org.
> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >>
> >
> >
> > _______________________________________________
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
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> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> >
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



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