be 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
tools that check and output the process
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 wrote:
>
>> Hi,
>>
>> can one ou
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 don'
x27;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 Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Bioph
ion.
> --
> 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 don't post (un)subscribe requests to the list. Use
4
> 14 2 -1( 16) 183.084 2.2030.9451.188
> 8 6 3
>
>
> Best performance was achieved with 16 PME nodes (see line 2)
> and original PME settings.
> Please use this command line to l
Hi,
On Sep 16, 2013, at 11:23 AM, mjyang 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 if it
ve 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
--
D
s" structures), and I'd like make an Umbrella Sampling
>>> calculation in order to study the PMF varying the distance between A and B.
>>>>>
>>>>> My problem is that I'd like fix the orientation of the axis of each
>>> structure A a
e in the z direction.
>>>
>>> It this possible? If it is so, could you tell me how to do that?
>>> Than you very much,
>>> Anna
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
&
>>>
>>> It this possible? If it is so, could you tell me how to do that?
>>> Than you very much,
>>> Anna
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>&
hive 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
--
On Apr 5, 2013, at 4:21 PM, Albert 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.
>>
On Apr 5, 2013, at 12:52 PM, Justin Lemkul 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=mpii
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 Kutzner
Max Planck Institute for Biophysical Chemistry
Theo
On Apr 2, 2013, at 5:47 PM, Albert 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 single precision.
B
; * Please 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/
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 don't post (un)subscribe requests to the list. Use the
> www interface or send
tp://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 K
Hi,
On Feb 6, 2013, at 6:03 PM, Richard Broadbent
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 sse4.1 and some (including the lo
On Dec 23, 2012, at 11:23 PM, Martin Hoefling 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 version that
support
the ab
http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please 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.
>
mally fastest 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 wrote:
>
>> Hi Chandan,
>>
> tuned for 24 ppn spanning across the two nodes.
>
> Chandan
>
>
> --
> Chandan kumar Choudhury
> NCL, Pune
> INDIA
>
>
> On Thu, Nov 29, 2012 at 8:32 PM, Carsten Kutzner wrote:
>
>> Hi Chandan,
>>
>> On Nov 29, 2012, at 3:30 PM, Chanda
e
> $g_tune_pme_4.5.5 -np 12 -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr
> -g tune.log -nice 0
> g_tune_pme executes on the head node and writes various files.
>
> Kindly let me know what am I missing when I submit through qsub.
>
> Thanks
>
> Chandan
> --
> C
> 1) Forces
> 2) Neighbor search (ok, going from 2cores to 4cores does not make a big
> differences, but from 1core to 2 or 4 saves much time)
>
> For GMX 4.0.7 ist looks similar, whereas the difference between 2 and 4 cores
> is not so high as for GMX 4.5.5
>
> Is there an
ch 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
/mailman/listinfo/gmx-users
> * Please 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 po
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 Kutzner
Max Planck Institute for Biophysical Chemistry
Theo
Hi,
On Oct 29, 2012, at 3:57 PM, Albert 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
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 Kutzner
Max Planck
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
ilman/listinfo/gmx-users
> * Only plain text messages are allowed!
> * Please 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...@g
upport/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 Kutzner
Max Planck Institute
@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Only plain text messages are allowed!
> * Please 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
h
>
> On 04/26/2012 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
>>
>>
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 tried many
> times with following co
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
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 e
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);
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
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
> #include
> at the head of the md.c
>
> but when i mak
,
do a ./bootstrap before the configure step.
Best,
Carsten
>
> Bests
>
> Da: Carsten Kutzner
> A: Alex Jemulin ; Discussion list for GROMACS users
>
> Inviato: Martedì 22 Novembre 2011 13:25
> Oggetto: Re: [gmx-users] do_dssp segmentation fault
>
> Dear Alex,
&g
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
> se
Hi,
On Aug 17, 2011, at 1:24 AM,
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 npme>nnodes is a bad setup, but a check would be nice.
cr->npmenodes is set in mdrun.c right after the
ling 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 don't post (un)subscribe requests to the list. Use the
> www interface or send i
;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 Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am
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
> e
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.
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 as
macs.org/mailman/listinfo/gmx-users
> Please 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
o/gmx-users
> Please 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.gro
On Feb 2, 2011, at 11:48 AM, lloyd riggs wrote:
> Dear Carsten Kutzner,
>
> First off, thanks. I did not specify it in the input md.mdp file, but when I
> looked at the generated out.mdp it had a Linear center of mass removal for
> the groups [system].
>
> When I add
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, 20
/gmx-users
> Please 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
ost (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 Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fass
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 Cami
n't post (un)subscribe requests to the list. Use thewww 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 C
arch 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 Kutzner
Max Planck Institute for Biophysical Chemist
if the questions are not made clear.
> Thank you.
>
> Best,
> Yanbin
> --
> 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 befor
P.O.box 13145-1384
> Tehran
> Iran
> http://www.ibb.ut.ac.ir/
> --
> 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
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 p
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:umbrella5
acs.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 Kutzner
Max Pla
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)" wrote:
>> Hello,
>>
>> I am trying to build Gromacs 4.5.3 using the Intel c
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 mai
/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 Kutzner
Max Planck Institute
Hi,
as a workaround you could run with -noappend and later
concatenate the output files. Then you should have no
problems with locking.
Carsten
On Nov 25, 2010, at 9:43 PM, Baofu Qiao wrote:
> Hi all,
>
> I just recompiled GMX4.0.7. Such error doesn't occur. But 4.0.7 is about 30%
> slower t
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
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:
>> Dea
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 noju
> Please 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/Suppo
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
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
> alloc
18) 1218.834 12.9310.884OK.
> Sander
>
> On 21 Oct 2010, 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 proc
still 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/ck
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 --pr
ers@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 don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-
t;
> Fax: +55 (16) 36024838
> Fone: +55 (16) 3602-3688/ 3602-4372
> e-mail: l...@obelix.ffclrp.usp.br
> l...@ffclrp.usp.br
>
>
> http://obelix.ffclrp.usp.br
>
>
>
>
>
> ________
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 won
t;> -- Checking for MSVC x86 inline asm
>> -- Checking for MSVC x86 inline asm - not supported
>> -- Checking for system XDR support
>> -- Checking for system XDR support - present
>> -- Using internal FFT library - fftpack
>> CMake Warning (dev) at CMakeLists.txt:6
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 Institut
/3.1/lib64/libmpigf.so: undefined reference to
> `PMPI_Add_error_code'
> /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to
> `PMPI_Comm_call_errhandler'
> /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to
> `PMPI_Type_get_extent'
> /opt/
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
>
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
> --
>
>gmx-users mailing listgmx-users@gromacs.org
><mailto:gmx-users@gromacs.org>
>
>http://lists.gromacs.org/mailman/listinfo/gmx-us
s, but there must be some more diagnostic 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 写道：
> Hi Justin,
>
> what kind of error message do you ge
gmx-users@gromacs.org
> > http://lists.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
e 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
Theoreti
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, 370
Dear Abdul,
please keep all Gromacs-related questions on the mailing list.
Best,
Carsten
Begin forwarded message:
> From: "abdul wadood"
> Date: July 3, 2010 8:40:29 AM GMT+02:00
> To:
> Subject: missing atom
>
> Dear Carsten
>
> I am running simulation using gromacs with amber forcefie
-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
iling listgmx-users@gromacs.org
> http://lists.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-requ...@gr
/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 fo
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 we
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 Kutzn
ot;Re: Contents of gmx-users digest..."
>
>
> Today's Topics:
>
>1. (no subject) (Amin Arabbagheri)
>2. Re: (no subject) (Justin A. Lemkul)
>3. Re: (no subject) (Linus ?stberg)
>4. Re: (no subject) (Carsten Kutzner)
>5. Help with defining new
nterface 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. +49-551-201
the lincs warning threshold
> in your mdp file
> 3: or set the environment variable GMX_MAXCONSTRWARN to -1,
> 3: but normally it is better to fix the problem
> 3: ---
> 3:
> Maybe your system is not well equilibrated, or your time step is too long.
>
> Carsten
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: --
x.
> Learn more. --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.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 int
1 - 100 of 226 matches
Mail list logo
