[gmx-users] pdb2gmx and terminal proline
David van der Spoel
spoel at xray.bmc.uu.se
Wed Nov 26 08:52:00 CET 2003
On Wed, 2003-11-26 at 08:21, Graham E Jackson wrote:
> Dear All,
> I have used pdb2gmx to convert a pdb file of a cyclic SS peptide built
> in INSIGHT. The peptide has an N-terminal proline. The command line I
> used was:
> pdb2gmx -f mol.pdb -o mol.gro -p mol.top -ss -ter -ignh
>
> Forcefield: 0 or 2 or 5
> Link Cys Cys: y
> N-term option: 1 (PRO-NH)
> C-term option: 2 (none)
>
> If I look at the structure generated with gOpenMol or vmd the NH of
> proline is linked to C6 with a very unusual bridging H. If I look at
> the topology file the H is only bonded to the proline N. However if I
> view the structure with ngmx the H is not bridging but the bond angles
> are all wrong for an sp3 N and the H is near C6.
>
You mean after energy minimization?
Can you send me the structure before and after EM?
> Any help?
>
> Graham.
>
> gmx-users-request at gromacs.org wrote:
> >
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> >
> > Today's Topics:
> >
> > 1. down with MPI (=?ISO-8859-1?B?Sm/jbyBDYXJsb3MgQw==?=amera Junior)
> > 2. Re: down with MPI (David van der Spoel)
> > 3. g_rdf (parinald at unsl.edu.ar)
> > 4. quick fix for g_covar? (barrett)
> > 5. multiple simulations (Nguyen Hoang Phuong)
> > 6. Re: multiple simulations (David van der Spoel)
> > 7. Re: CVS version (gilles)
> > 8. Re: quick fix for g_covar? (Berk Hess)
> > 9. Re: Re: quick fix for g_covar? (Ruben Martinez Buey)
> > 10. Re: quick fix for g_covar? (Berk Hess)
> > 11. Re: Imaging Problem (Ilya Chorny)
> > 12. Re: replica exchange (Luca Monticelli)
> > 13. Re: replica exchange (Ilya Chorny)
> > 14. Re: g_rdf (Dallas Warren)
> > 15. Problem on processing proteins consisting of two chains (wang chuanming)
> >
> > --__--__--
> >
> > Message: 1
> > Date: Tue, 25 Nov 2003 10:17:19 -0200
> > From: =?ISO-8859-1?B?Sm/jbyBDYXJsb3MgQw==?=amera Junior <camera at df.ibilce.unesp.br>
> > To: gmx-users at gromacs.org
> > Subject: [gmx-users] down with MPI
> > Reply-To: gmx-users at gromacs.org
> >
> > Hi,
> >
> > When i running my mdrun in a beowulf cluster with 16 nodes, the network
> > down in a few hours. What can be wrong?
> >
> > thanks in advanced,
> >
> > -------------------------------------------------
> > This mail sent through IMP: http://horde.org/imp/
> >
> > --__--__--
> >
> > Message: 2
> > Subject: Re: [gmx-users] down with MPI
> > From: David van der Spoel <spoel at xray.bmc.uu.se>
> > To: gmx-users at gromacs.org
> > Organization:
> > Date: 25 Nov 2003 13:35:28 +0100
> > Reply-To: gmx-users at gromacs.org
> >
> > On Tue, 2003-11-25 at 13:17, =?ISO-8859-1?B?Sm/jbyBDYXJsb3MgQw==?=amera
> > Junior wrote:
> > > Hi,
> > >
> > > When i running my mdrun in a beowulf cluster with 16 nodes, the network
> > > down in a few hours. What can be wrong?
> > >
> > anything.
> > be more specific, but you may have to ask somewhere else.
> > >
> > > thanks in advanced,
> > >
> > >
> > > -------------------------------------------------
> > > This mail sent through IMP: http://horde.org/imp/
> > > _______________________________________________
> > > gmx-users mailing list
> > > gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please don't post (un)subscribe requests to the list. Use the
> > > www interface or send it to gmx-users-request at gromacs.org.
> > --
> > David.
> > ________________________________________________________________________
> > David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > Husargatan 3, Box 596, 75124 Uppsala, Sweden
> > phone: 46 18 471 4205 fax: 46 18 511 755
> > spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
> > --__--__--
> >
> > Message: 3
> > Date: Tue, 25 Nov 2003 10:07:11 -0300 (ART)
> > From: <parinald at unsl.edu.ar>
> > To: gmx-users at gromacs.org
> > Subject: [gmx-users] g_rdf
> > Reply-To: gmx-users at gromacs.org
> >
> > Hello gmx`ers:
> > I have Cl- and Na+ en water, how I can do the rdf
> > to: Oxigen with Cl-, Oxigen with Na+, Hidrogen with Na+, Hidrogen
> > with CL-?
> > Thank you. Pablo.
> >
> > --__--__--
> >
> > Message: 4
> > From: "barrett" <barrett at biop.ox.ac.uk>
> > To: <gmx-users at gromacs.org>
> > Date: Tue, 25 Nov 2003 13:24:58 -0000
> > Subject: [gmx-users] quick fix for g_covar?
> > Reply-To: gmx-users at gromacs.org
> >
> > The fix to write_xpm3 described in the attached link would be very
> > useful to me.
> >
> > http://www.gromacs.org/pipermail/gmx-developers/2003-July/000539.html
> >
> > We have an existing 3.1.4 build which I don't really want to recompile
> > from scratch. The only use I really have for this at the moment is the
> > g_covar command to get xpm files. Is there an easy way of getting an
> > updated g_covar by itself?
> >
> > (running on PC cluster running Redhat linux)
> >
> > many thanks
> >
> > Paul
> >
> > Dr Paul Barrett
> > Laboratory of Molecular Biophysics
> > Department of Biochemistry
> > University of Oxford
> > Oxford
> > OX1 3QU
> >
> > Tel 01865 275380
> > Fax 01865 275182
> >
> > barrett at biop.ox.ac.uk
> > hellopaul1 at hotmail.com
> >
> > --__--__--
> >
> > Message: 5
> > Date: Tue, 25 Nov 2003 14:25:55 +0100 (MET)
> > From: Nguyen Hoang Phuong <phuong at theochem.uni-frankfurt.de>
> > To: gmx-users at gromacs.org
> > Subject: [gmx-users] multiple simulations
> > Reply-To: gmx-users at gromacs.org
> >
> > Dear All,
> >
> > what is the meaning of the option -multi in mdrun program?
> >
> > I thought that with this option, multiple simluations will run in
> > parallel. However, I get only one simulation is run. I did as the following
> >
> > grompp -f md1.mdp -c md1.gro -p x.top -o md1.tpr -np 1
> > grompp -f md2.mdp -c md2.gro -p x.top -o md2.tpr -np 1
> >
> > mdrun -multi -np 2 -s md1.tpr md2.tpr
> >
> > but only the simulation with md1.tpr is run.
> >
> > What the problem is?
> >
> > Phuong
> >
> > --__--__--
> >
> > Message: 6
> > Subject: Re: [gmx-users] multiple simulations
> > From: David van der Spoel <spoel at xray.bmc.uu.se>
> > To: gmx-users at gromacs.org
> > Organization:
> > Date: 25 Nov 2003 14:33:48 +0100
> > Reply-To: gmx-users at gromacs.org
> >
> > On Tue, 2003-11-25 at 14:25, Nguyen Hoang Phuong wrote:
> > > Dear All,
> > >
> > > what is the meaning of the option -multi in mdrun program?
> > >
> > > I thought that with this option, multiple simluations will run in
> > > parallel. However, I get only one simulation is run. I did as the following
> > >
> > > grompp -f md1.mdp -c md1.gro -p x.top -o md1.tpr -np 1
> > > grompp -f md2.mdp -c md2.gro -p x.top -o md2.tpr -np 1
> > >
> > > mdrun -multi -np 2 -s md1.tpr md2.tpr
> > >
> > > but only the simulation with md1.tpr is run.
> > >
> > > What the problem is?
> > you still need to run with mpirun
> >
> > >
> > > Phuong
> > >
> > > _______________________________________________
> > > gmx-users mailing list
> > > gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please don't post (un)subscribe requests to the list. Use the
> > > www interface or send it to gmx-users-request at gromacs.org.
> > --
> > David.
> > ________________________________________________________________________
> > David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > Husargatan 3, Box 596, 75124 Uppsala, Sweden
> > phone: 46 18 471 4205 fax: 46 18 511 755
> > spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
> > --__--__--
> >
> > Message: 7
> > Date: Tue, 25 Nov 2003 15:54:00 +0100 (CET)
> > From: gilles <gilles at chem.rug.nl>
> > To: <gmx-users at gromacs.org>
> > Subject: Re: [gmx-users] CVS version
> > Reply-To: gmx-users at gromacs.org
> >
> > Hi Alan,
> >
> > automake 1.7.x does not work with the current cvs snapshot, you have to
> > use automake 1.5.x instead to create your Makefile.
> >
> > Gilles
> >
> > On Fri, 31 Oct 2003, Alan Wilter Sousa da Silva wrote:
> >
> > > Hi List!
> > > I need help to compiled cvs version.
> > > I never had problem before. But now I'm having problems. I also took a
> > > look at Mailing-List archives, but I didn't get much.
> > >
> > > I'm using Mandrake 9.1 and had to install autoconf2.5-2.57-3mdk
> > > e automake1.6-1.7.2-3mdk.
> > >
> > > automake (GNU automake) 1.7.2
> > >
> > > autoconf (GNU Autoconf) 2.57
> > >
> > > Now running ./bootstrap I got:
> > >
> > > -----------------------------------------------
> > > ./bootstrap
> > > share/template/Makefile.am:16: CFLAGS was already defined in condition
> > > TRUE, which implies condition DOUBLE_TRUE ...
> > > configure.ac:211: ... `CFLAGS' previously defined here.
> > > share/template/Makefile.am:18: CFLAGS was already defined in condition
> > > TRUE, which implies condition DOUBLE_FALSE ...
> > > src/tools/Makefile.am: object `lsq.$(OBJEXT)' created both with libtool
> > > and without
> > > src/tools/Makefile.am: object `dlist.$(OBJEXT)' created both with libtool
> > > and without
> > > ------------------------------------------------
> > > Anyway, a configure file is generated.
> > >
> > > Now running ./configure:
> > >
> > > ------------------------------------------------
> > > ./configure
> > > [... ok]
> > > checking if the C compiler supports inline assembly... yes
> > > configure: error: conditional "am__fastdepCXX" was never defined.
> > > Usually this means the macro was only invoked conditionally.
> > > ------------------------------------------------
> > >
> > > So I got no Makefile!
> > >
> > > Any help here, please!
> > >
> > > Cheers,
> > >
> > > --------------------------
> > > Alan Wilter Sousa da Silva
> > > --------------------------
> > > B.Sc. - Dep. Física - UFPA
> > > M.Sc. - Dep. Física - PUC/RJ
> > > D.Sc. - IBCCF/UFRJ
> > > Bolsista Pesquisador LAC-INPE
> > > São José dos Campos (SP), Brasil
> > > www.lac.inpe.br/~alan
> > > _______________________________________________
> > > gmx-users mailing list
> > > gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please don't post (un)subscribe requests to the list. Use the
> > > www interface or send it to gmx-users-request at gromacs.org.
> > >
> >
> > --
> >
> > ------------------------------------------------------------------------
> > | Hi! I'm a .signature virus! |
> > | Copy me into your ~/.signature to help me spread! |
> > ------------------------------------------------------------------------
> > |Gilles Pieffet |
> > |Molecular Dynamics Group |
> > |Dept. of Biophysical Chemistry |
> > |University of Groningen |
> > |Nijenborgh 4 |
> > |9747 AG Groningen |
> > |The Netherlands |
> > |_______________________________________________|
> >
> > --__--__--
> >
> > Message: 8
> > From: "Berk Hess" <gmx3 at hotmail.com>
> > To: gmx-users at gromacs.org
> > Subject: [gmx-users] Re: quick fix for g_covar?
> > Date: Tue, 25 Nov 2003 15:58:15 +0100
> > Reply-To: gmx-users at gromacs.org
> >
> > >Is there an easy way of getting an updated g_covar by itself?
> > >
> > >(running on PC cluster running Redhat linux)
> > >
> > >many thanks
> > >
> > >Paul
> >
> > I sent you a binary by email.
> > This new g_covar of the soon to be release 3.2.0 version also calculates
> > the covariance matrix in a more accurate way.
> >
> > Berk.
> >
> > _________________________________________________________________
> > Protect your PC - get McAfee.com VirusScan Online
> > http://clinic.mcafee.com/clinic/ibuy/campaign.asp?cid=3963
> >
> > --__--__--
> >
> > Message: 9
> > Date: Tue, 25 Nov 2003 16:38:13 +0100
> > From: Ruben Martinez Buey <ruben at akilonia.cib.csic.es>
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] Re: quick fix for g_covar?
> > Reply-To: gmx-users at gromacs.org
> >
> > Hi Berk,
> > Where can I get this new g_covar?
> > Thanks in advance
> > best wishes,
> > Ruben
> >
> > Berk Hess wrote:
> >
> > >> Is there an easy way of getting an updated g_covar by itself?
> > >>
> > >> (running on PC cluster running Redhat linux)
> > >>
> > >> many thanks
> > >>
> > >> Paul
> > >
> > >
> > > I sent you a binary by email.
> > > This new g_covar of the soon to be release 3.2.0 version also calculates
> > > the covariance matrix in a more accurate way.
> > >
> > > Berk.
> > >
> > > _________________________________________________________________
> > > Protect your PC - get McAfee.com VirusScan Online
> > > http://clinic.mcafee.com/clinic/ibuy/campaign.asp?cid=3963
> > >
> > > _______________________________________________
> > > gmx-users mailing list
> > > gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please don't post (un)subscribe requests to the list. Use the www
> > > interface or send it to gmx-users-request at gromacs.org.
> > >
> > >
> >
> > --
> > PLEASE NOTE NEW ADDRESS AND PHONE/FAX NUMBERS
> >
> > Ruben Martínez-Buey. PhD student.
> > Protein Function and Structure
> > Centro de Investigaciones Biológicas
> > Consejo Superior de Investigaciones Científicas
> > C/ Ramiro de Maeztu, 9
> > 28040 Madrid (SPAIN)
> > phone:34-918373112 ext 4380
> > fax: 34-915360432
> >
> > --__--__--
> >
> > Message: 10
> > From: "Berk Hess" <gmx3 at hotmail.com>
> > To: gmx-users at gromacs.org
> > Subject: [gmx-users] Re: quick fix for g_covar?
> > Date: Tue, 25 Nov 2003 16:49:49 +0100
> > Reply-To: gmx-users at gromacs.org
> >
> > >Hi Berk,
> > >Where can I get this new g_covar?
> > >Thanks in advance
> > >best wishes,
> > >Ruben
> >
> > By getting the cvs code, or by waiting a few weeks for the release of
> > Gromacs 3.2.0.
> >
> > I just remembered that you can obtain the covariance matrix in an ascii file
> > using
> > g_covar -debug
> > (also in Gromacs 3.1)
> > Maybe this should be a standard option.
> >
> > Berk.
> >
> > _________________________________________________________________
> > MSN Search, for accurate results! http://search.msn.nl
> >
> > --__--__--
> >
> > Message: 11
> > Subject: Re: [gmx-users] Imaging Problem
> > From: Ilya Chorny <ichorny at maxwell.compbio.ucsf.edu>
> > To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> > Organization:
> > Date: 25 Nov 2003 09:24:28 -0800
> > Reply-To: gmx-users at gromacs.org
> >
> > Could someone please take a look at my posting. I am attempting to do
> > umbrella sampling but this is a bug that was supposed to be fixed
> > according to the postings. Should I download the CVS version of gromacs?
> >
> > Ilya
> >
> > On Mon, 2003-11-24 at 11:48, Ilya Chorny wrote:
> > > Hello
> > >
> > > I ran a distance restraint calculation between two molecules where I
> > > kept the distance between two of the atoms fixed. I had some strange
> > > results and when I watched the trajectory using VMD I noticed that when
> > > one of the molecules left the box it got moved to the other side as one
> > > would expect but the distance between the molecules also changed to the
> > > geometric distance and not the min image distance. Am I making some
> > > mistake in setting up the calculation.
> > >
> > >
> > > Thanks
> > >
> > > Ilya
> > >
> > > cpp = /lib/cpp
> > > integrator = md
> > > constraints = all-bonds
> > > dt = 0.002 ; ps !
> > > nsteps = 500000 ; total 10 ps.
> > > nstcomm = 1
> > > nstenergy = 100
> > > nstlist = 1
> > > coulombtype = PME
> > > rlist = .9
> > > rcoulomb = .9
> > > rvdw = .9
> > > Tcoupl = nose-hoover
> > > tc-grps = SOL COO AGG
> > > tau_t = 0.1 0.1 .1
> > > ref_t = 300 300 300
> > > ; Energy monitoring
> > > ; Pressure coupling is not on
> > > Pcoupl = berendsen
> > > tau_p = 0.5
> > > compressibility = 6.0e-6
> > > ref_p = 1.0
> > > ; Generate velocites is on at 300 K.
> > > gen_vel = yes
> > > gen_temp = 300.0
> > > gen_seed = 173529
> > > ; distance restraints
> > > disre = simple
> > > disre_weighting = equal
> > > nstdisreout = 10
> > >
> > >
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > gmx-users mailing list
> > > gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please don't post (un)subscribe requests to the list. Use the
> > > www interface or send it to gmx-users-request at gromacs.org.
> >
> > --__--__--
> >
> > Message: 12
> > Date: Tue, 25 Nov 2003 16:23:41 -0700
> > From: Luca Monticelli <lmonti at ucalgary.ca>
> > To: gmx-users at gromacs.org
> > Cc: gmx-developers at gromacs.org
> > Subject: Re: [gmx-users] replica exchange
> > Reply-To: gmx-users at gromacs.org
> >
> > Hi Ilya,
> >
> > I've been working on a replica exchange
> > version of gromacs together with Walter
> > Ash (also in Peter Tieleman's group).
> > The code seems to be working, but we are
> > still testing it; also, we think there
> > are still a few things that need to be
> > fixed, and we prefer not to release the
> > code until we make sure it does not
> > contain stupid errors.
> > It's not my highest priority project
> > (same for Walter), but I think we'll be
> > able to release a beta version by the
> > end of the year (hopefully).
> > Anyway, if you want to use scripts
> > (instead of a modified code) it's going
> > to be really straightforward.
> >
> > Cheers,
> >
> > luca
> >
> > Ilya Chorny wrote:
> > > Has anyone done replica exchange in gromacs. (i.e written the scripts to
> > > due replica exchange). It seems like it would be pretty straight forward
> > > but I don't want to reinvent the wheel if its already been invented.
> > >
> > > Thanks
> > >
> > > Ilya
> >
> > --
> > ___________________________________
> >
> > Luca Monticelli, PhD
> > Department of Biological Sciences
> > University of Calgary
> > 2500 University Drive NW
> > Calgary, AB, T2N 1N4, Canada
> > e-mail: lmonti at ucalgary.ca
> > Phone: (403) 220-2264
> > Fax: (403) 289-9311
> > ___________________________________
> >
> > --__--__--
> >
> > Message: 13
> > Subject: Re: [gmx-users] replica exchange
> > From: Ilya Chorny <ichorny at maxwell.compbio.ucsf.edu>
> > To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> > Organization:
> > Date: 25 Nov 2003 15:54:19 -0800
> > Reply-To: gmx-users at gromacs.org
> >
> > Hi Luca,
> >
> > That sounds great. I have not started writing the scripts because my
> > simulations are getting good sampling at one temp, but I was thinking
> > about future calculations.
> >
> > Thanks
> >
> > Ilya
> >
> >
> > On Tue, 2003-11-25 at 15:23, Luca Monticelli wrote:
> > > Hi Ilya,
> > >
> > > I've been working on a replica exchange
> > > version of gromacs together with Walter
> > > Ash (also in Peter Tieleman's group).
> > > The code seems to be working, but we are
> > > still testing it; also, we think there
> > > are still a few things that need to be
> > > fixed, and we prefer not to release the
> > > code until we make sure it does not
> > > contain stupid errors.
> > > It's not my highest priority project
> > > (same for Walter), but I think we'll be
> > > able to release a beta version by the
> > > end of the year (hopefully).
> > > Anyway, if you want to use scripts
> > > (instead of a modified code) it's going
> > > to be really straightforward.
> > >
> > > Cheers,
> > >
> > > luca
> > >
> > >
> > >
> > > Ilya Chorny wrote:
> > > > Has anyone done replica exchange in gromacs. (i.e written the scripts to
> > > > due replica exchange). It seems like it would be pretty straight forward
> > > > but I don't want to reinvent the wheel if its already been invented.
> > > >
> > > > Thanks
> > > >
> > > > Ilya
> > >
> >
> > --__--__--
> >
> > Message: 14
> > Date: Wed, 26 Nov 2003 12:44:09 +1100
> > From: Dallas Warren <dallas.warren at vcp.monash.edu.au>
> > Subject: Re: [gmx-users] g_rdf
> > To: gmx-users at gromacs.org
> > Reply-To: gmx-users at gromacs.org
> >
> > > I have Cl- and Na+ en water, how I can do the rdf
> > >to: Oxigen with Cl-, Oxigen with Na+, Hidrogen with Na+, Hidrogen
> > >with CL-?
> >
> > Generate an index file (make_ndx) that has groups of Cl-, Na+, OW and HW1 +
> > HW2. Then run g_rdf for each of the pairs of groups you are interested in
> > for a given trajectory.
> >
> > Catch ya,
> >
> > Dr. Dallas Warren
> > Research Fellow
> > Department of Pharmaceutical Biology and Pharmacology
> > Victorian College of Pharmacy, Monash University
> > 381 Royal Parade, Parkville VIC 3010
> > dallas.warren at vcp.monash.edu.au
> > +61 3 9903 9083
> > --------------------------------------------------------------------------
> > When the only tool you own is a hammer, every problem begins to resemble a nail.
> >
> > --__--__--
> >
> > Message: 15
> > From: "wang chuanming" <chuanmingwang at hotmail.com>
> > To: gmx-users at gromacs.org
> > Date: Wed, 26 Nov 2003 14:05:24 +0800
> > Subject: [gmx-users] Problem on processing proteins consisting of two chains
> > Reply-To: gmx-users at gromacs.org
> >
> > Dear all,
> > I am a new user of Gromacs.I am trying to do a simulation on a protein
> > which consists of two chains(A and B) like HIV PR.Unfortunately, the two
> > chains got far away from each other. I found that two itp
> > files(protein_A.itp and protein_B.itp) were generated after using pdb2gmx.
> > It seems that Gromacs recognizes the two chains as different proteins,but
> > they belong to the same molecule indeed.
> > How can I resolve the problem? Your experiences on Gromacs will helful
> > for me.
> >
> > _________________________________________________________________
> > ÓëÁª»úµÄÅóÓѽøÐн»Á÷£¬ÇëʹÓà MSN Messenger: http://messenger.msn.com/cn
> >
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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