Hi,
I would like to measure the Hydrophobic and Hydrophilic components of
the Solvent Accessible Surface Area. In the Tool Changes for 5.0 I found
these command:
gmx sasa -s md.tpr -f md_traj.trr -surface 'group "A"' -output
'"Hydrophobic" group "A" and charge {-0.2 to 0.2}; "Hydrophilic" group
Hi All,
We are currently in the process of benchmarking GROMACS5.1.2 on our local
HPC systems. There are some nice results posted online
(http://www.gromacs.org/@api/deki/files/240/=gromacs-5.0-benchmarks.pdf). I
was wondering if anybody can kindly share the files (such as, pdbs, mdps,
tops and
Good Morning,
I am a graduate student at the University of Colorado at Boulder. The
University is in the process of transitioning to a new supercomputer and
the Research Computing team who is in charge of setting it up said that
they would be happy to benchmark Gromacs on the computer if I
To: oliwias; gmx-us...@gromacs.org
Cc: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] gromacs 5.0 tools: gmx distance and gmx mindist
time series
Hi,
On Thu, May 7, 2015 at 3:59 PM oliwias oliw...@ethz.ch wrote:
1. How can I get rid of the inconsistency? Did I use
Dear All,
I am trying to use the new gromacs 5.0 tools for analysis. I tried
multiple options but I can't get gmx distance and gmx mindist to print
out time series of distances. I only get the average. On the other hand,
I had no problem with getting the time series with gromacs 4.6 g_dist
Hi,
Time series are what gmx distance does... see gmx distance -h, of course.
If it's not working for you, you'll have to tell us exactly what you tried,
what output you got, what's not suitable, etc., and check that your input
files contain what you think they do (e.g. with gmx check)
Mark
On
Hi Mark,
I'm quite new to gromacs, so thanks for your help! I have an md
trajectory in 3 files. I used:
gmx_trjcat -f md1.xtc md2.xtc md3.xtc -o md.xtc -settime
in order to get one file for analysis. I set the time of the first file
to 0.0, and for the next two files I set the time to c
Hi,
On Thu, May 7, 2015 at 3:59 PM oliwias oliw...@ethz.ch wrote:
1. How can I get rid of the inconsistency? Did I use the wrong options
for gmx_trjcat?
Depends whether you care. You wrote files with two different output
periods, and now you want to treat them as a continuous thing, which in
...@gromacs.org
Subject: Re: [gmx-users] Gromacs 5.0 compilation slower than 4.6.5.
What
wentwrong ?
This cutoff-scheme difference is probably caused by using an .mdp file
that
does not specify the cutoff scheme, and the default changed in 5.0.
grompp
issued a note about this, if you go
...@gromacs.org
Subject: Re: [gmx-users] Gromacs 5.0 compilation slower than 4.6.5. What
wentwrong ?
This cutoff-scheme difference is probably caused by using an .mdp file
that
does not specify the cutoff scheme, and the default changed in 5.0.
grompp
issued a note about this, if you go
Dear Gromacs users,
I just compiled gromacs 5.0 with the same compiler (gcc 4.7.2), same OS
(RHEL 6) same configuration options and basically everything than my
previous gromacs 4.6.5 compilation and when doing one of our typical
simulations, I get worst performance.
4.6.5 does 45 ns/day
5.0
Please post the command lines you used to invoke mdrun as well as the
log files of the runs you are comparing.
Cheers,
--
Szilárd
On Fri, Sep 5, 2014 at 12:10 PM, David McGiven davidmcgiv...@gmail.com wrote:
Dear Gromacs users,
I just compiled gromacs 5.0 with the same compiler (gcc 4.7.2),
Command line in both cases is :
1st : grompp -f grompp.mdp -c conf.gro -n index.ndx
2nd :mdrun -nt 48 -v -c test.out
Log file you mean the standard output/error ? Attached to the email ?
Thanks
2014-09-05 12:30 GMT+02:00 Szilárd Páll pall.szil...@gmail.com:
Please post the command
Thanks Szilard, here it goes! :
4.6.5 : http://pastebin.com/nqBn3FKs
5.0 : http://pastebin.com/kR4ntHtK
2014-09-05 12:47 GMT+02:00 Szilárd Páll pall.szil...@gmail.com:
mdrun writes a log file, named md.log by default, which contains among
other things results of hardware detection and
Hello,
From the log files it is clear that out of 48 cores, the 5.0 run had 8
cores allocated to PME while the 4.6.5 run had 12 cores. This seems to have
caused a greater load imbalance in case of the 5.0 run.
If you notice the last table in both .mdp files, you will notice that the
PME
Hi Abhi,
Yes I noticed that imbalance but I thought gromacs knew better than the
user how to split PP/PME!!
How is it possible that 4.6.5 guesses better than 5.0 ?
Anyway, I tried :
mdrun -nt 48 -v -c test.out
Exits with an error You need to explicitly specify the number of MPI
threads
What is even more strange is that I tried with 10 pme nodes (mdrun -ntmpi
48 -v -c TEST_md.gro -npme 16), got a 15,8% performance loss and ns/day are
very similar : 33 ns/day
D.
2014-09-05 14:54 GMT+02:00 David McGiven davidmcgiv...@gmail.com:
Hi Abhi,
Yes I noticed that imbalance but I
Hi,
you might want to use g_tune_pme to find out the optimal number
of PME nodes for 4.6 and 5.0.
Carsten
On 05 Sep 2014, at 15:39, David McGiven davidmcgiv...@gmail.com wrote:
What is even more strange is that I tried with 10 pme nodes (mdrun -ntmpi
48 -v -c TEST_md.gro -npme 16), got a
Hello,
Is you system solvated with water molecules?
The reason I ask is that, in case of the run with 4.6.5 you gromacs has
used a group cut-off scheme, whereas 5.0 has used verlet scheme. For system
with water molecules, group scheme gives better performance than verlet.
For more check out:
This cutoff-scheme difference is probably caused by using an .mdp file that
does not specify the cutoff scheme, and the default changed in 5.0. grompp
issued a note about this, if you go and check it. The change in the -npme
choice is a direct consequence of this; the heuristics underlying the
users gmx-us...@gromacs.org
Subject: Re: [gmx-users] Gromacs 5.0 compilation slower than 4.6.5. What
wentwrong ?
This cutoff-scheme difference is probably caused by using an .mdp file that
does not specify the cutoff scheme, and the default changed in 5.0. grompp
issued a note about this, if you go
for maintaining
both schemes is indeed poor.
Mark
Thanks.
Regards,
Abhishek
-Original Message-
From: Mark Abraham mark.j.abra...@gmail.com
Sent: 9/5/2014 7:57 PM
To: Discussion list for GROMACS users gmx-us...@gromacs.org
Subject: Re: [gmx-users] Gromacs 5.0 compilation slower than 4.6.5
imbalance
Cheers,
--
Szilárd
Could you please shed little light on this ?
Thanks.
Regards,
Abhishek
-Original Message-
From: Mark Abraham mark.j.abra...@gmail.com
Sent: 9/5/2014 7:57 PM
To: Discussion list for GROMACS users gmx-us...@gromacs.org
Subject: Re: [gmx-users] Gromacs
Dear gromacs users,
I am compiling Gromacs 5.0, but can't find how to enable compiling with
QMMM funtion like ORCA.
would you please tell me how to get it ?
Jun Gao
Shandong University
--
Gromacs Users mailing list
* Please search the archive at
Hi. I am not a expert but looking the CMakeLists.txt
Did you try the argument cmake ... *-DGMX_QMMM_PROGRAM=orca* ../gromacs
Maybe that works
Good luck
On Wed, Sep 3, 2014 at 2:40 AM, 高军 gao...@sdu.edu.cn wrote:
Dear gromacs users,
I am compiling Gromacs 5.0, but can't find how to
Hi everyone,
I'm trying to install Gromacs 5.0 on a computer which has no network
connection.
It would be appreciated if some one tell me how this can be done!
Regards
Fatemeh
--
Gromacs Users mailing list
* Please search the archive at
Hello. Just take the .tar.gz on a thumb drive to your new machine and install
from that.
Note that this machine will already need to have all the prerequisites. If not,
you will need to install those first:
cmake
gcc
Don’t forget fftw lapack and blas. You can use the ones built in gromacs with
Good morning,
I am trying to compile gromacs 5.0 using the intel 14.0 compiler, but I
receive the following error early in the compilation process:
catastrophic error: #error directive: -- unsupported ICC
configuration! Only ICC 13.1 on Linux x86_64 is supported!
Although I can obtain
Ah...I see now that it is in fact the cuda compiler that is complaining.
Thanks!
David
On 07/30/2014 01:07 PM, Szilárd Páll wrote:
That's the nvcc, the CUDA compiler (officially) not supporting
anything, but that very version of the Intel compilers. I suggest you
use a recent gcc, the
Hey Mark,
This might be a a dumb question, but over the official release download
links on the gromacs website, it still says: Please note that these are
not yet regarded as production quality, pending further testing, but the
code is now feature-stable.
Is this a typo because I thought the
On Jul 2, 2014 6:44 PM, Ali Khan ak...@virginia.edu wrote:
Hey Mark,
This might be a a dumb question, but over the official release download
links on the gromacs website, it still says: Please note that these are
not yet regarded as production quality, pending further testing, but the
code
I know this is a silly question but in the downloads section when I click
to download it the new window opens and 0bit tar file is downloaded.I
switched to windows but even then the new tab doesn't show anything.I don't
understand why is this happening.
--
Gromacs Users mailing list
* Please
The link is correct, something must be broken on your side. Try using e.g. wget:
$ wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz ls -l gromacs*.gz
--2014-07-02 22:34:44-- ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz
= `gromacs-5.0.tar.gz'
Resolving
Maybe something on your end is blocking ftp connections. You can download
from a mirror such as:
http://fossies.org/linux/privat/gromacs-5.0.tar.gz
If you download from a mirror make sure to check the md5sum.
On Wed, Jul 2, 2014 at 4:36 PM, Szilárd Páll pall.szil...@gmail.com wrote:
The link
Yeah apparently the ftp connection is blocked.I actually forgot that.Thanks
for the help.
On Thu, Jul 3, 2014 at 2:16 AM, Roland Schulz rol...@utk.edu wrote:
Maybe something on your end is blocking ftp connections. You can download
from a mirror such as:
On 7/2/14, 4:36 PM, Szilárd Páll wrote:
The link is correct, something must be broken on your side. Try using e.g. wget:
$ wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz ls -l gromacs*.gz
--2014-07-02 22:34:44-- ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz
=
On Wed, Jul 2, 2014 at 11:08 PM, Justin Lemkul jalem...@vt.edu wrote:
On 7/2/14, 4:36 PM, Szilárd Páll wrote:
The link is correct, something must be broken on your side. Try using e.g.
wget:
$ wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz ls -l
gromacs*.gz
--2014-07-02
I ran the md5sum but it does not match with any of the hashes.What should I
do now?
On Wed, Jul 2, 2014 at 5:55 PM, Szilárd Páll pall.szil...@gmail.com wrote:
On Wed, Jul 2, 2014 at 11:08 PM, Justin Lemkul jalem...@vt.edu wrote:
On 7/2/14, 4:36 PM, Szilárd Páll wrote:
The link is
On Wed, Jul 2, 2014 at 6:55 PM, Harshkumar Singh harshsingh2...@gmail.com
wrote:
I ran the md5sum but it does not match with any of the hashes.What should I
do now?
Which file from which server (/which URL) did you download? What md5 did
you get?
Roland
On Wed, Jul 2, 2014 at 5:55 PM,
Hi GROMACS users,
The official release of GROMACS 5.0 is available!
What new things can you expect?
* GROMACS now uses a combination of *C++98* and C99, so you will need a
working C++ compiler that is intended to work with your C compiler
* Building GROMACS now requires *CMake version 2.8.8*,
I haven't used membed with v5.0, but in v4.6.5 you make a text file with
the options that you can still find in the legacy g_membed help
documentation: http://manual.gromacs.org/online/g_membed.html
e.g. a file with something like:
nxy = 1000
nz = 0
Hi,
the g_membed tool is integrated in mdrun now. Try
gmx mdrun -membed membed.dat
Best,
Carsten
On 30 Apr 2014, at 03:41, gejingming 531015...@qq.com wrote:
dear sir,
now ,I am using gromacs 5.0 VERSION ,but there is not g_membed and tpbconv
commond.I think it is important for us.can
dear sir,
now ,I am using gromacs 5.0 VERSION ,but there is not g_membed and tpbconv
commond.I think it is important for us.can you add these commond to the new
version.
thank you!
gjm
--
Gromacs Users mailing list
* Please search the archive at
On 4/29/14, 9:41 PM, gejingming wrote:
dear sir,
now ,I am using gromacs 5.0 VERSION ,but there is not g_membed and tpbconv
commond.I think it is important for us.can you add these commond to the new
version.
g_membed has been removed, so you'll have to use an older version that includes
Hi GROMACS users,
The second beta release of GROMACS 5.0 is available! We are making this
available to you to get an early taste of how GROMACS 5.0 will look and
work, and most importantly to get feedback from you about how well things
work. While we try our hardest to keep the quality of GROMACS
On 29.01.2014 11:15, Mark Abraham wrote:
* lots of internal cleaning of the house
* various bug fixes
Status report on windows:
Build Perfectly!
Builds error-free out-of-the-box using
Visual C++ 2012 (VC11), cmake 2.8.12.1,
Cuda 5.5, already installed Boost 1.55,
already installed
On 29.01.2014 15:06, Mirco Wahab wrote:
A test run (martini small vesicle system,
250K atoms) did start promising but crashed
after 15 min without any indication. (I'll
try without gpu later).
I identified the problem. It is the same problem
that also required a patch in the 4.6.x versions
on
Hi,
I uploaded fixes for both issues:
https://gerrit.gromacs.org/#/c/3040/
https://gerrit.gromacs.org/#/c/3041/
Thanks for the feedback.
Roland
On Wed, Jan 29, 2014 at 12:59 PM, Mirco Wahab
mirco.wa...@chemie.tu-freiberg.de wrote:
On 29.01.2014 15:06, Mirco Wahab wrote:
A test run
Thanks. It'd be nice if MSVC did what it claims to do, and create more
pages on demand for such allocations.
Mark
On Wed, Jan 29, 2014 at 6:59 PM, Mirco Wahab
mirco.wa...@chemie.tu-freiberg.de wrote:
On 29.01.2014 15:06, Mirco Wahab wrote:
A test run (martini small vesicle system,
250K
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