Re: [gmx-users] GPU-gromacs

to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel

[gmx-users] Output pinning for mdrun

Hi, can one output how mdrun threads are pinned to CPU cores? Thanks, Carsten -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please

Re: [gmx-users] Output pinning for mdrun

placement for a dummy parallel job, or environment variables like MP_INFOLEVEL for loadleveler. Thanks! Carsten Mark On Thu, Oct 24, 2013 at 11:44 AM, Carsten Kutzner ckut...@gwdg.de wrote: Hi, can one output how mdrun threads are pinned to CPU cores? Thanks, Carsten -- gmx-users

Re: [gmx-users] parallelization

interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49

Re: [gmx-users] MPI runs on a local computer

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Re: [gmx-users] performance issue with the parallel implementation of gromacs

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Re: [gmx-users] question about installation parameters

Hi, On Sep 16, 2013, at 11:23 AM, mjyang mjy...@hku.hk wrote: Dear GMX users, I have a question about the combination of the installation parameters. I compiled the fftw lib with --enable-sse2 and configured the gromacs with cmake .. -DGMX_CPU_ACCELERATION=SSE4.1. I'd like to know

Re: [gmx-users] Umbrella sampling simulations using make_edi with -restrain and -harmonic

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Re: [gmx-users] Rotation Constraints - PMF - external potential

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Re: [gmx-users] Rotation Constraints - PMF - external potential

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Re: [gmx-users] Rotation Constraints - PMF + rerun

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Re: [gmx-users] Rotation Constraints - PMF

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Re: [gmx-users] Intel compiling failed

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Re: [gmx-users] Intel compiling failed

On Apr 5, 2013, at 12:52 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/5/13 6:38 AM, Carsten Kutzner wrote: Hi Albert, one reason for the error you see could be that you are using a non-Intel MPI compiler wrapper. I think you need to specify MPICC=mpiicc as well. Is there any

Re: [gmx-users] Intel compiling failed

On Apr 5, 2013, at 4:21 PM, Albert mailmd2...@gmail.com wrote: On 04/05/2013 12:38 PM, Carsten Kutzner wrote: Hi Albert, one reason for the error you see could be that you are using a non-Intel MPI compiler wrapper. I think you need to specify MPICC=mpiicc as well. Carsten thanks

Re: [gmx-users] 4.6.1 support double precision GPU now?

On Apr 2, 2013, at 5:47 PM, Albert mailmd2...@gmail.com wrote: Hello: I am wondering is double precision supported in current 4.6.1 GPU version? Otherwise it would be very slow to use CPU version running free energy calculations…. Hi Albert, no, GPU calculations can be done only in

Re: [gmx-users] g_tune_pme can't be executed

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Re: [gmx-users] Mismatching number of PP MPI processes and GPUs per node

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Re: [gmx-users] compiling on different architecture than the compute nodes architecture

Hi, On Feb 6, 2013, at 6:03 PM, Richard Broadbent richard.broadben...@imperial.ac.uk wrote: Dear All, I would like to compile gromacs 4.6 to run with the correct acceleration on the compute nodes on our local cluster. Some of the nodes have intel sandy-bridge whilst others only have

Re: [gmx-users] voltage for membrane?

On Dec 23, 2012, at 11:23 PM, Martin Hoefling martin.hoefl...@gmail.com wrote: You can have a look at http://www.ncbi.nlm.nih.gov/pubmed/21843471 , maybe that does what you want. On http://www.mpibpc.mpg.de/grubmueller/compel you will find installation instructions for the special gromacs

Re: [gmx-users] Essential dynamics (ED) sampling using make_edi

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Re: [gmx-users] g_tune_pme for multiple nodes

. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Thu, Nov 29, 2012 at 8:32 PM, Carsten Kutzner ckut...@gwdg.de wrote: Hi Chandan, On Nov 29, 2012, at 3:30 PM, Chandan Choudhury iitd...@gmail.com wrote: Hi Carsten, Thanks for your suggestion. I did try to pass

Re: [gmx-users] g_tune_pme for multiple nodes

unless you could have all PME processes exclusively on a single node. Carsten Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Tue, Dec 4, 2012 at 6:39 PM, Carsten Kutzner ckut...@gwdg.de wrote: Hi Chandan, the number of separate PME nodes in Gromacs must be larger than

Re: [gmx-users] g_tune_pme for multiple nodes

and writes various files. Kindly let me know what am I missing when I submit through qsub. Thanks Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Mon, Sep 3, 2012 at 3:31 PM, Carsten Kutzner ckut...@gwdg.de wrote: Hi Chandan, g_tune_pme also finds the optimal number

Re: [gmx-users] Re: Question about scaling

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Re: [gmx-users] Question about scaling

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Re: [gmx-users] GROMACS with different gcc and FFT versions but one unique *tpr file

search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr. Carsten

Re: [gmx-users] Regarding g_tune_pme optimization

it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http

Re: [gmx-users] too much warnings and notes

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Re: [gmx-users] too much warnings and notes

Hi, On Oct 29, 2012, at 3:57 PM, Albert mailmd2...@gmail.com wrote: On 10/29/2012 03:56 PM, Carsten Kutzner wrote: Hi, find the reason for the warnings in your mdp file settings and adjust them accordingly. You can also override the warnings with the -maxwarn number option in grompp

Re: [gmx-users] Ion conduction through a protein-membrane system

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Re: [gmx-users] g_tune_pme cannot be executed

interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax

Re: [gmx-users] g_tune_pme for multiple nodes

requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen

Re: [gmx-users] how to optimize performance of IBM Power 775?

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Re: [gmx-users] how to run g_tune_pme in cluster?

09:53 AM, Carsten Kutzner wrote: Hi, what output does g_tune_pme provide? What is in log and in perf.out? Can it find the correct mdrun / mpirun executables? Carsten On Apr 26, 2012, at 9:28 AM, Albert wrote: Hello: Does anybody have any idea how to run g_tune_pme in a cluster? I

Re: [gmx-users] Error: 4095 characters, fgets2 has size 4095

Hi Steven, you might have to remove files with weird names (such as ._name) in the directory where you run grompp or in your forcefield directory. Carsten On Apr 10, 2012, at 11:52 AM, Steven Neumann wrote: Dear Gmx Users, It is 1st time I came across such problem. While preparing my

Re: [gmx-users] another g_tune_pme problem

On Apr 1, 2012, at 8:01 PM, Albert wrote: Hello: I am trying to test g_tune_pme in workstation by command: g_tune_pme_d -v -s md.tpr -o bm.trr -cpi md.cpt -cpo bm.cpt -g bm.log -launch -nt 16 but it stopped immediately with following logs. I complied gromacs with a -d in each

Re: [gmx-users] Scaling/performance on Gromacs 4

Hi Sara, my guess is that 1500 steps are not at all sufficient for a benchmark on 64 cores. The dynamic load balancing will need more time to adapt the domain sizes for optimal balance. It is also important that you reset the timers when the load is balanced (to get clean performance numbers);

Re: [gmx-users] Is there a way to omit particles with, q=0, from Coulomb-/PME-calculations?

Hi Thomas, Am Jan 17, 2012 um 10:29 AM schrieb Thomas Schlesier: But would there be a way to optimize it further? In my real simulation i would have a charged solute and the uncharged solvent (both have nearly the same number of particles). If i could omit the uncharged solvent from the

Re: [gmx-users] modify the gromacs4.5.5 code: using cout

Use fprintf(stdout, …); Carsten On Nov 30, 2011, at 12:27 PM, 杜波 wrote: dear teacher, i want to modify the gromacs4.5.5 code ,can i use function cout which is introuduce in c++. i add the code #include string.h #include iostream at the head of the md.c but when i

Re: [gmx-users] do_dssp segmentation fault

before the configure step. Best, Carsten Bests Da: Carsten Kutzner ckut...@gwdg.de A: Alex Jemulin alexbioi...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Inviato: Martedì 22 Novembre 2011 13:25 Oggetto: Re: [gmx-users] do_dssp segmentation fault Dear

Re: [gmx-users] do_dssp segmentation fault

Dear Alex, On Nov 22, 2011, at 9:28 AM, Alex Jemulin wrote: Dear all I'm experiencing the following error in Gromacs 4.5 with do_dssp Here is the command do_dssp -f md.xtc -s md.tpr -o secondary-structure.xpm -sc secondary-structure.xvg -dt 10 give me the following error

Re: [gmx-users] suggestion that mdrun should ensure npme the numberof processes

Hi, On Aug 17, 2011, at 1:24 AM, chris.ne...@utoronto.ca chris.ne...@utoronto.ca wrote: Currently, gromacs4.5.4 gives a segfault if one runs mpirun -np 8 mdrun_mpi -npme 120 with no warning of the source of the problem. Obviously npmennodes is a bad setup, but a check would be nice.

Re: [gmx-users] g_tune_pme

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Re: [gmx-users] GROMACS 4.5.1 mdrun re-compile for MPI

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Re: [gmx-users] New maintenance release: gromacs-4.5.4

Hi, try to add the --disable-shared flag to your invocation of .configure. Carsten On Mar 22, 2011, at 3:26 PM, Ye MEI wrote: Thank you for the new version of gromacs. But the compilation of gromacs failed on my computer. The commands are as follows: make distclean export CC=icc export

Re: [gmx-users] Performance in ia64 and x86_64

Hello Ignacio, On Feb 25, 2011, at 10:25 AM, Ignacio Fernández Galván wrote: Well, I've compiled mdrun with MPI (with fortran kernels in the ia64), and run my test system in both machines, with a single processor. The results are still worrying (to me). This is a 50 time step (0.5

Re: [gmx-users] GROMACS installation query

On Feb 23, 2011, at 6:16 AM, Tom Dupree wrote: Greetings all, I am new to Linux and wish to confirm some facts before I press on with the installation. In the installation guide, http://www.gromacs.org/Downloads/Installation_Instructions There is a line saying “...Where assembly

Re: [gmx-users] configure: error: cannot compute sizeof (off_t)

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Re: [gmx-users] Performance in ia64 and x86_64

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Re: [gmx-users] General MD question

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Re: [gmx-users] segmentation fault: g_velacc

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Re: [gmx-users] segmentation fault: g_velacc

Hi Vigneshwar, the problem is fixed now in the release-4-0-patches branch. Carsten On Feb 1, 2011, at 2:00 PM, Carsten Kutzner wrote: Hi, apparently this bug fix made it to 4.5, but not to 4.0. I will apply the fix also there. Carsten On Feb 1, 2011, at 1:58 PM, Justin A. Lemkul

Re: [gmx-users] Re: Gromacs + GPU: Problems running dppc example in ftp://ftp.gromacs.org/pub/benchmarks/gmxbench-3.0.tar.gz

Hi Camilo, On Jan 27, 2011, at 7:19 AM, Camilo Andrés Jimenez Cruz wrote: Sorry, abrupt sending, the coulombtype is the same coulombtype = cut-off Is your cut-off actually 0.0 then? Carsten and constraints = all-bonds is the same. Any idea? 2011/1/27 Camilo

Re: [gmx-users] 4 x Opteron 12-core or 4 x Xeon 8-core ?

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Re: [gmx-users] gromacs 4.5.3 with threads instead of MPI

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Re: [gmx-users] g_tune_pme big standard deviation in perf.out output

to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany

Re: [gmx-users] stopping mdrun without error massage

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Re: [gmx-users] how to add a electric field to the water box when do a simulation

On Dec 20, 2010, at 12:09 PM, 松啸天 wrote: dear: I would like to use the electric field inside a box defined by gromacs. So I added E_x 1 10 0in the .mdp file, is it the right approach? Yes, this will add an electric field of strength 10 V/nm acting in x-direction. Carsten i hope

Re: [gmx-users] pullx.xvg / pullf.xvg

On Dec 16, 2010, at 2:23 PM, Poojari, Chetan wrote: Hi, Following were the commands which i used in the umbrella sampling simulations: grompp -f md_umbrella.mdp -c conf500.gro -p topol.top -n index.ndx -o umbrella500.tpr mdrun -v -deffnm umbrella500 Output:umbrella500.xvg,

Re: [gmx-users] g-WHAM

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Re: [gmx-users] problem building Gromacs 4.5.3 using the Intel compiler

Hi, you might also need to use the mpiicc compiler wrapper instead of the mpicc to enforce using icc instead of gcc. Carsten On Dec 13, 2010, at 2:20 PM, Mark Abraham wrote: On 12/13/10, Miah Wadud Dr (ITCS) w.m...@uea.ac.uk wrote: Hello, I am trying to build Gromacs 4.5.3 using the

[gmx-users] Re: trouble parallelizing a simulation over a cluster

On Dec 8, 2010, at 1:03 PM, Hassan Shallal wrote: Thanks a lot Justin for the very helpful answers concerning the pressure equilibration. Using Berendsen Barostat over 200 ps has lead to the correct average pressure... I have another issue to discuss with you and with the Gromacs mailing

Re: [gmx-users] How to suppress the error X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group

...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http

Re: [gmx-users] installation

On Nov 24, 2010, at 4:04 PM, Rossella Noschese wrote: Hi all, I'm trying to install gromacs.4.5.3 on fedora 13. I followed the instruction on the website, I completed my make install and this was the output: GROMACS is installed under /usr/local/gromacs. Make sure to update your PATH and

Re: [gmx-users] unexpexted stop of simulation

Hi, there was also an issue with the locking of the general md.log output file which was resolved for 4.5.2. An update might help. Carsten On Nov 3, 2010, at 3:50 PM, Florian Dommert wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 11/03/2010 03:38 PM, Hong, Liang wrote: Dear

Re: [gmx-users] Fwd: -pbc nojump

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Re: [gmx-users] Fwd: -pbc nojump

On Oct 27, 2010, at 10:05 AM, leila karami wrote: Hi Carsten Thanks for your answer. You got my case very well. I understand your mean as follows: 1) Trjconv –f a.xtc –s a.tpr –o b.xtc –pbc mol (output group=water) 2) Trjconv –f a.xtc –s a.tpr –o c.xtc –pbc nojump

Re: [gmx-users] g_dipole ? =salt-molecule = Does Gromacs consider counter ions?

On Oct 22, 2010, at 4:14 PM, Chih-Ying Lin wrote: Hi Sorry, I ask the same question again because i am not a decent person in this field. If possible, someone can give me a quick answer while i am trying to get understanding the source codes. My basic understanding is that Gromacs has

[gmx-users] Gromacs 4.5.1 on 48 core magny-cours AMDs

seem to be migrating around. Carsten -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne

Re: [gmx-users] Gromacs 4.5.1 on 48 core magny-cours AMDs

, at 12:03 , Carsten Kutzner wrote: Hi, does anyone have experience with AMD's 12-core Magny-Cours processors? With 48 cores on a node it is essential that the processes are properly pinned to the cores for optimum performance. Numactl can do this, but at the moment I do not get good

Re: [gmx-users] Gromacs 4.5.1 on 48 core magny-cours AMDs

On Oct 21, 2010, at 4:44 PM, Sander Pronk wrote: Thanks for the information; the OpenMPI recommendation is probably because OpenMPI goes to great lengths trying to avoid process migration. The numactl doesn't prevent migration as far as I can tell: it controls where memory gets allocated

Re: [gmx-users] Error on install Gromacs 4

On Oct 20, 2010, at 5:17 AM, Son Tung Ngo wrote: Dear experts, I have just install gromacs 4.5.1 on my cluster (using CentOS that was install openmpi1.5, Platform MPI, fftw3, g77, gcc , g++) but I have problem with size of int : [r...@icstcluster gromacs-4.5.1]# ./configure

Re: [gmx-users] MPI and dual-core laptop

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[gmx-users] Re: efficient use of pme with gromacs

l...@ffclrp.usp.br http://obelix.ffclrp.usp.br Sent via the WebMail system at srv1.ffclrp.usp.br -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational

Re: [gmx-users] git gromacs

Hi Alan, 'bleeding edge' gromacs development is as always in the 'master' branch. The latest bugfixes for the 4.5.x versions you are going to find in the 'release-4-5-patches' branch. Carsten On Sep 7, 2010, at 12:09 PM, Alan wrote: Hi there, Now that gromacs 4.5.1 is released I was

Re: [gmx-users] Problem with installing mdrun-gpu in Gromacs-4.5

interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49

Re: [gmx-users] help with git

/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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Carsten Kutzner

Re: [gmx-users] decomposition

Hi Jacopo, from somewhere the information about the 7 nodes must have come. What are the exact commands you used? What MPI are you using? Carsten On Jul 26, 2010, at 12:35 PM, Jacopo Sgrignani wrote: Dear all i'm trying to run a MD simulation using domain decomposition but after two days

Re: [gmx-users] Installing gromacs from git

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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Carsten Kutzner Max Planck Institute

Re: [gmx-users] P4_error for extending coarse grained MD simulations

-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http

Re: [gmx-users] P4_error for extending coarse grained MD simulations

information from mdrun about what has gone wrong. Please check stderr / stdout output files as well as md.log. Carsten Justin Zhang 在 2010年7月9日 下午4:00，Carsten Kutzner ckut...@gwdg.de写道： Hi Justin, what kind of error message do you get if you run this system on a single core without MPI

Re: [gmx-users] mpi run

. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home

Re: [gmx-users] mdrun_mpi: error while loading shared libraries: libimf.so: cannot open shared object file: No such file or directory

-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http

[gmx-users] Fwd: missing atom

Dear Abdul, please keep all Gromacs-related questions on the mailing list. Best, Carsten Begin forwarded message: From: abdul wadood wadoodbiochem...@hotmail.com Date: July 3, 2010 8:40:29 AM GMT+02:00 To: ckut...@gwdg.de Subject: missing atom Dear Carsten I am running simulation

Re: [gmx-users] ED sampling

before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical

Re: [gmx-users] the job is not being distributed

before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical

Re: [gmx-users] the job is not being distributed

On Jun 28, 2010, at 2:34 PM, Syed Tarique Moin wrote: hello, I am running a simulation on dual core processor using the following command mpirun -np 8 mdrun_mpi -s top The job is running but it is not distributed on other node, i mean i cant see the process on other nodes as well. I

Re: [gmx-users] the job is not being distributed

)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077

Re: [gmx-users] Should I use separate PME nodes

http://www.gromacs.org/mailing_lists/users.php -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne

Re: [gmx-users] Re: gmx-users Digest, Vol 74, Issue 134

: (no subject) (Carsten Kutzner) 5. Help with defining new residue (OXY--HEME) (Omololu Akin-Ojo) 6. Re: Help with defining new residue (OXY--HEME) (Justin A. Lemkul) -- Message: 1 Date: Mon, 21 Jun 2010 05:00:04 -0700

Re: [gmx-users] (no subject)

://www.gromacs.org/mailing_lists/users.php -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users

[gmx-users] Re: Parallel instalation: gmx-users Digest, Vol 74, Issue 76

, or your time step is too long. Carsten Hotmail is redefining busy with tools for the New Busy. Get more from your inbox. See how. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel

[gmx-users] Re: Parallel instalation: gmx-users Digest, Vol 74, Issue 76

On Jun 17, 2010, at 3:42 PM, abdul wadood wrote: Dear Carsten the command which i give is mpiexec -l -np 4 /usr/local/gromacs/bin/mdrun_mpi -s topol.tpr with this command the same error come which is Can not open file: 3: topol.tpr 3:

Re: [gmx-users] Parallel installation

://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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry

Re: [gmx-users] question about how to install g_tune_pme

posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational

Re: [gmx-users] DSSP

Hi Shahid, I have fixed the problem in do_dssp. You can either pull the newest release-4-0-patches branch from the git repository or change ./src/tools/do_dssp.c, line 80 from snew(ssbuf,nres+10); to: snew(ssbuf, 2*nres-1); Carsten On May 19, 2010, at 9:48 AM, Carsten Kutzner wrote: Hi

Re: [gmx-users] DSSP

post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp

Re: [gmx-users] very low speed in simulation !( need for help)

the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313

Re: [gmx-users] make_edi, g_covar -nofit

that was produced by the first command? You have to do the checkout --track in the directory where a .git subdir is present. git clone git://git.gromacs.org/gromacs.git cd gromacs git checkout --track -b release-4-0-patches origin/release-4-0-patches Carsten -- Dr. Carsten Kutzner Max Planck

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