Re: [gmx-users] infelicity in installation of 4.0.2

the output of ldd $your_executable? Have you sourced the GMXRC file? Greetings, Florian -- ------- Dr. Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen

Re: [gmx-users] Re: problems running grompp with protein-ligand complex

t AMBER analytical function > ; i j k l func phase kd pn > 16 11 14 15 1 180.00 4.60240 2 ;C35- C39- C37- H38 > (more text not sent) > > [ system ] > M_E > > [ molecules ] > ; Compoundnmols > M_E 1 > __

Re: [gmx-users] grace/xmgace

hd i do. > whether there is some another technique by which i can get it. > > Bhawana greetings, Florian -- ------- Dr. Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ N

Re: [gmx-users] Box size

> Or can I specify somehow the box coordinates (vector lenghts and > angles) already when I run pdb2gmx? No, you need start editconf > > Thank you in advance for any contribution. > > Best regards, > Andrea Greetings, Florian -- --------

Re: [gmx-users] do_dssp

uld set an environment variable DSSP pointing to the dssp executable, e.g.: setenv DSSP /opt/dssp/bin/dssp Greetings, Florian -- ------- Dr. Florian Haberl Computer-Chemie-Centrum Universitaet

Re: [gmx-users] two pdb files

arks line and perhaps cahnge numbering. > > Does anybody know how to do it? > > Or the same with .gro files? > > Thanks. > > Vitaly > Greetings, Florian -- ------- Dr. Florian Haberl

Re: [gmx-users] Converting 2-d molecule to 3-D

sers > > 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 [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/

Re: [gmx-users] how to make h-bond existence map?

tings, Florian > > On Wed, 03 Sep 2008 Florian Haberl wrote : > >Hi, > > > >On Wednesday, 3. September 2008, minnale wrote: > > > Thanks Justin for your valuable suggestions > > > I have done the way you suggested. I gave command like this > >

Re: [gmx-users] how to make h-bond existence map?

/2201650/1?PARTNER=3&OAS > >>_QUERY=null> > >> > >> > >> > >> > >>___ > >>gmx-users mailing listgmx-users@gromac

Re: [gmx-users] M*tif installation

ng! Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- --- F

Re: [gmx-users] Genion failing in parallel runs.

; System is "protein in water", dodecahedron box. Everything is fine till > energy minimisation. genion is failing. > > Any clue?? > > Thanks. greetings, Florian -- --- Florian Haberl

Re: [gmx-users] g_hbond output analysis

e or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php greetings, Florian -- ------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nue

Re: [gmx-users] colour of the molecules

ttp://www.gromacs.org/mailing_lists/users.php greetings, Florian -- ----------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0)

Re: [gmx-users] Please help: POPC membrane simulation

s > newbie greetings, Florian -- ------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26573 M

Re: [gmx-users] plotting displacement of each C-alpha along first eigenvector having largest eigenvalue

cipation greetings, Florian -- ----------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26573 Mailto: florian.ha

Re: [gmx-users] dimerization problem

n with position restraints to get a valid structure for a free MD simulation. See the wiki for the normal simulation protocol ( http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation ) greetings, Florian --

Re: [gmx-users] amb2gmx for big systems

rc Cientific de Barcelona > > > > _ > Herramientas para combatir la crisis. MSN Dinero > http://dinero.es.msn.com/ Greetings, Florian -- ---

Re: [gmx-users] Analysis of mutants

ke g_rms g_dist ... Greetings, Florian -- ----------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26573 Mailto

Re: [gmx-users] make_ndx problem

used force field. Also "h" prints out some inforamation about the selection choices. greetings, Florian -- ------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nue

Re: [gmx-users] drawing chemicals 2d sketchs

at features I would appreciate very > much your help. > > Many thanks in advance. > Alan greetings, Florian -- ----------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlan

Re: [gmx-users] Re:: Specified frame doesn't exist or file not seekable

he problem, but there's almost no value in writing > >XTC input in .trr format on output. > > > >* I have found few discussions in gmx-archives regarding this problem and > > *>* due to BUG in source code its showing error. > * Greetings, Florian --

Re: [gmx-users] extract conformations !!

gt; >Please tell me the solution of my this problem > > Thanks > Anamika Greetings, Florian -- ------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlan

Re: [gmx-users] RMSD plot

> > > >Justin A. Lemkul > > >Graduate Research Assistant > > >Department of Biochemistry > > >Virginia Tech > > >Blacksburg, VA > > >[EMAIL PROTECTED] | (540) 231-9080 > > >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ > > > &g

Re: [gmx-users] Making PDB file

> > Alex Greatings, Florain -- ----------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26573

Re: [gmx-users] Help for GNUPlot

"gyrate.xvg" > ^ > Bad data on line 9 > > gnuplot> > Regards, > Lal badshah > > Send instant messages to your online friends http://uk.messenger.yahoo.com take a look on your data file less rmsf.xvg first 12 lines or so are without

Re: [gmx-users] (no subject)

Florian -- --- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26573 Mailto: florian.haberl AT chemie.uni-er

Re: [gmx-users] gromacs analysis performance on a dual core suse box.

low nfs server are the limiting factor. Greetings, Florian -- ----------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +

Re: [gmx-users] MPICH 1.2 vs. GMX 4.0

send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- --- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91

Re: [gmx-users] Re: Dose the GROMOS FF favour beta-sheets?

al, Adam; Gelpí, Josep Lluis; Orozco, Modesto A consensous view to Protein Dynamics Proc. Natl. Acad. Sci USA (2007), 104, 796-801. Greetings, Florian -- ----------- Florian Haberl Computer-Chem

Re: [gmx-users] Abnormal fluctuation in RMSD

173529 > > > Thanking you > > With best regards > Anamika you are using PBC and your system is sometimes jumping out of the box, so you have to mirror it back to its normal box trjconv -f yourtraj.trr -o yourtraj_fit.trr -s topol.tpr -pbc nojump should fix it a

Re: [gmx-users] gromacs versus amber boxsize -correction-

; 110.5103716 > > This is makes a hugde difference in the number of water atoms to add. > Does anyone has an explanation for this paradox? so you generate two different boxsizes or types. > > > kind regards, > > servaas greetings, Florian -- -----

Re: [gmx-users] normal mode analysis

romacs.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 [EMAIL PROTECTED] > Can't post? Read http:

Re: [gmx-users] karthik

d from where one more thing is to how to install using tar.gz > Your linux installation is without fftw, you have to install it first. http://wiki.gromacs.org/index.php/Installation greetings, Florian -- -------

Re: [gmx-users] How can I add hydrogen?

y protonate -h Greetings, Florian -- ------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 8

Re: [gmx-users] Problem in downloading source code

tp://www.gromacs.org/search before > > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > -- > raja > [EMAIL PROTECTED]

Re: [gmx-users] MPIRUN problem when switched to 8 np (searched the list)

options for mpirun must be added > (-nolocal, -machinefile, $PBS_NODESFILE) > now I'm trying to follow the steps in the webpage you gave to me > > On 10/1/07, Florian Haberl <[EMAIL PROTECTED]> wrote: > > Hi, > > > > On Sunday, 30. September 2007 19:12,

Re: [gmx-users] MPIRUN problem when switched to 8 np (searched the list)

; gmx-users mailing listgmx-users@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

Re: [gmx-users] how to remove periodicity when using g_rmsd

... > > Thank you > > Tang jiaowei Greetings, Florian -- ----------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone

Re: [gmx-users] Average Structure outputted from g_rmsf

post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php Greetings, Florian -- --- Florian Ha

Re: [gmx-users] New single thread performance numbers

> larger cache. > > > > Still, it's very nice to see that AMD is at least back on the field > > again. Let's hope for an aggressive frequency ramp-up and a price > > war ;-) > > > > Cheers, > > > > Erik > > > > On Sep 17, 2

[gmx-users] New single thread performance numbers

orian -- --- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26581 Mailto: florian.haberl AT chemie.uni-erlang

Re: [gmx-users] psf 2 top

o/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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php Greetings,

Re: [gmx-users] floating exception

groups to a smaller number our change your analysis computer. > > > Jiaowei Tang Greetings, Florian -- ------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg

Re: [gmx-users] gromacs mdrun problems

something like: not found you can try source GROMACSDIR/bin/GMXRC > > any help in this in much appreciated > many thanks > Jonathan Spicer Greetings, Florian -- ------- Florian Haberl

Re: [gmx-users] Correlation Matrix Calculation

cs from Lange and Grubmueller: http://www.mpibpc.gwdg.de/groups/grubmueller/start/people/olange/gencorr.html > > Much thanks, > > Arneh greetings, Florian -- ----------- Florian Haberl Comput

Re: [gmx-users] a question about make_ndx

se the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php greetings, florian -- --- Florian Haberl Computer-Chemie-Centrum Un

Re: [gmx-users] Appropriate command for measuring density of the whole simulation box along the trajectory

posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ------- Fl

Re: [gmx-users] Can I convert Amber (.prepin) into Gromacs (.itp) topology?

transfer it to .gro and .top file with gromacs format. You also need to take the correct forcefield of AMBER. > > Or, is gromacs has tool that generate topology parameters like antechamber > in amber? > > Thank you for reading. Greetings, Florian -- ------

Re: [gmx-users] a problem in the energy minimization.the

r vdw > constraints   =   none ;no constraint > pbc   =   no ; no periode boundary conditions > > Best wishes! greetings, Florian -- --- Florian Haberl Computer-Chemie-Centrum Universitaet Erla

Re: [gmx-users] viewing .xvg plots in windows environment

greetings, Florian -- ----------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26581 Mai

Re: [gmx-users] Suggestion needed for new workstation

gmx-users@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 [EMAIL PROTECTED] > Can&

Re: [gmx-users] Install GROMACS - Deb package

gt; Thanks! Greetings, florian -- ----------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26581 Mailto: floria

Re: [gmx-users] GRomacs 3.3.1 parallel run

Finished is set > > What could be the origin of this problems? > > Thank you very much > > Fabio > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users

Re: [gmx-users] Is there a way to compile gromacs with MPICH instead of LAM?

t. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php Greetings, Florian -- ----------- Florian Haberl Co

Re: [gmx-users] Error running grompp

/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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php Greetings, Flori

Re: [gmx-users] RNA ffgmx.hdb problems

ease don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php \ Greetings, Florian -- --- Florian Haberl

Re: [gmx-users] do_dssp: main chain

for your reply, Justin. Indeed I had chosen 'Protein' so far. But > it is not evident that this caused the problem, since it worked well in > some cases. Indeed, choosing 'MainChain' (indeed index group 5) does not > help, but results in the same behavior. > > Volker Greetings,

Re: [gmx-users] how to find out the average running structure

ard. Greetings, Florian -- ----------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26581 Mailto: florian.haber

Re: [gmx-users] change the ligand in pdb file

[EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052

Re: [gmx-users] Human Serum Albumin problem

post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- --- Florian Haberl C

Re: [gmx-users] xmgrace

WChem. open it with your favourite text editor, if its ascii you can use xmgrace for making plots, also gnuplot will work. These programms can open any file extensions. > > Best wishes, > > Michal Walczak Grettings, Florian -- ---

Re: [gmx-users] GROMACS Wiki

t to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php Greetings, Florian -- --- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/

Re: [gmx-users] RMSD

n (matrix) so you should have than an 10x10 matrix so also RMSD of 1 to 2, 1 to 3 ... greetings, florian -- ----------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naege

Re: [gmx-users] do_dssp crashes on certain machines..

gt; 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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php Grettings, Florian -- --

Re: [gmx-users] Preliminary report on benchmark on Opteron Cluster Infiniband on current CVS version

--with-fft=fftw3 \ > --without-xml --disable-threads \ > --with-external-blas --with-external-lapack > > # Configure for the MPI version of mdrun program: > ./configure --prefix=$PWD/gromax4_${TARGET} \ > --enable-mpi --program-suffix=_${MPIMODULE} \ > --with-fft=fftw3 \ >

[gmx-users] other output format of Matrix Data than xpm format

, Florian -- --- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26581 Mailto: florian.haberl AT

Re: [gmx-users] Running GROMACS in PBS

rch before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php Greetings, Florian -- ---

Re: [gmx-users] GROMOS vs. Amber

ards, > > Michal W. -- ------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26581 Mailto: flor

Re: [gmx-users] RMSD of the same protein in different solvent boxes

; Fale com seus amigos de graça com o novo Yahoo! Messenger > http://br.messenger.yahoo.com/ greetings, Florian -- ----------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuern

Re: [gmx-users] analyze an md run

cs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php Greetings, Florian -- -------

[gmx-users] Re: gromacs and pH description!

t; every chemical reactions! how can i do that? > > Thanks alot > > > - > 8:00? 8:25? 8:40? Find a flick in no time > with theYahoo! Search movie showtime shortcut. -- ------- Florian Haberl

Re: [gmx-users] N/A

to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php Greetings, Florian -- --- Florian Haberl Comp

Re: [gmx-users] trjconv(extraction of certain frames)

s to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php Greetings, Florian -- ----------- Florian Haberl Computer-

Re: [gmx-users] energy

;t post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ----------- Florian Haberl

Re: [gmx-users] g_hbond

@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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php Greetings, Florian -- -----

Re: [gmx-users] AMBER atom type for Hydroxamate moeity

000 ; N2 sp2 N in amino groups > amber99_3914.01000 ; N3 sp3 N for charged amino groups > (Lys, etc) > amber99_4014.01000 ; N* sp2 N > > > > With thanks! > B.Nataraj > -- > raja > [EMAIL PROTECTED] Greetings,

[gmx-users] calculating energy for more than 256 index groups

in the log file there are only interactions calculated for the first 256 energy groups. what do i have to change also or is this somewhere an hard limit? greetings, Florian -- --- Florian Haberl

Re: [gmx-users] gromacs instillation

from install of gromacs-3.3-1 > conflicts with file from package mono-web-1.1.13.7-6 Something is broken in your installation. Easiest thing is to compile gromacs from scratch as the gromacs faq say. Greetings, Florian -- ---

Re: [gmx-users] system net charge 0f -1.6

NOTE: > System has non-zero total charge: -1.80e+01 > > > I tried adding C term Oxygen with spdbv as well, but it still the same > uneven charge. > > What happened? > > thanks in advance > > Stefan Florian -- --

Re: [gmx-users] g_sdf now uploaded to website

7;t post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php Greetings, Florian -- --- Florian Haberl

Re: [gmx-users] pca on amber MD output

w.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php Greetings, Florian --

Re: [gmx-users] execution of water tutorial files on BG/L

> > ___ > > gmx-users mailing listgmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don't post (un)s

Re: [gmx-users] Installation of Gromacs into BG/L

`/project2/gaussden/fujisaki/src/gromacs-3.3.1/src/kernel' make[2]: *** > [all-recursive] Error 1 > make[2]: Leaving directory > `/project2/gaussden/fujisaki/src/gromacs-3.3.1/src' make[1]: *** [all] > Error 2 > make[1]: Leaving directory > `/project2

Re: [gmx-users] Re: Question about parallazing Gromacs (Qiao Baofu)

> gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/user

Re: [gmx-users] Question about parallazing Gromacs

> gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/

Re: [gmx-users] CVS password

x27;t post? Read http://www.gromacs.org/mailing_lists/users.php Greetings, Florian -- --- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telep

Re: [gmx-users] merge ligand and protein

the answers take a look at http://www.gromacs.org/gromacs/documentation/tutorial.html John Kerrigans drug/enzyme tutorial and another GROMACS intro > > Best Regard > Kanin -- ------- Florian Haberl

Re: [gmx-users] amber ff and cpp error message

On Monday 04 September 2006 11:40, Florian Haberl wrote: > Hi, > > i got a strange behaviour of amberff implementation in gromacs > (http://folding.stanford.edu/ffamber/): > > cpp is not running without problems or warnings: is in faq as e.sorin mailed me http://folding.st

[gmx-users] amber ff and cpp error message

usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/include /usr/include End of search list Greetings, Florian -- ----------- Florian Haberl Computer-Chemie-Centrum Universitaet Erla

[gmx-users] analyses of g_hbond

orian -- --- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26581 Mailto: florian.haberl AT chemi

Re: [gmx-users] mdrun_hole problem

on't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php Greetings, Florian -- --- Florian Haber

Re: [gmx-users] Req for computer config for windows to run gromacs

AIL PROTECTED] Greetings, Florian -- ------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26581 Mailto: flor

Re: [gmx-users] [EMAIL PROTECTED] on PS3 == Gromacs on PS3?

http://www.gromacs.org/mailing_lists/users.php > > ___________ > gmx-users mailing listgmx-users@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

Re: [gmx-users] nr2nametop

http://www.gromacs.org/mailing_lists/users.php -- ----------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26581 Ma

Re: [gmx-users] renumtop

p://www.gromacs.org/mailing_lists/users.php -- ----------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26581 Mailt

Re: [gmx-users] Re: problem with gromacs on cluster

bove > > your installation is probably fine. > you have to tell mpirun to use more than one node, try "man mpirun" > Next step is to get a queing system like pbs/maui for your cluster, which puts all jobs on the nodes. > > please ask further questions on the mailing list

[gmx-users] Benchmarks for woodcrest cpu

-- --- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26581 Mailto: florian.haberl AT chemie.uni-erlangen.de

Re: [gmx-users] MPI gromacs usage

nce of the shared memory system use mpi mpt (it s sgi mpich version) to compile and run it. Greetings, Florian -- ----------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernbe

Re: [gmx-users] Problems with g_anaeig!

be requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php Greetings, Florian -- --- Florian H

Re: [gmx-users] Gromacs on Pathscale/Infiniband?

ace or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php Greetings, Florian -- --- Florian Haberl Computer-Chemie-

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