On 05.11.2013 10:04, sarah k wrote:
I'm going to perform a molecular dynamics simulation on a protein. As a
default the simulation gives one final *.gro file. I need to get a .gro
file after each say 500 ps of my simulation, in addition of the final file.
How can I do so?
Riccardo already gave
On 11.09.2013 09:38, shahid nayeem wrote:
I checked in folder
/cygdrive/c/packages/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3.a
, this file exists but perhaps `src/gmxlib/cyggmx_d-8.dll' is not able to
locate it.
Did you 'cmake' with -DGMX_PREFER_STATIC_LIBS=ON ?
BTW,
On 10.09.2013 08:20, shahid nayeem wrote:
I am installing gromacs -4.6.3 on cygwin with following commands
tar -xvzf gramcs-4.6.3.tar.gz
cd gromacs-4.6.3
mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_DOUBLE=on
It runs fine and write file in build directory.
when I run make
On 25.07.2013 04:25, Carlos Bueno wrote:
I added all the repositories and installed all you told me.
And that solved the problem for one of the computers
The others still have an error in make:
[ 55%] Building NVCC (Device) object
src/mdlib/nbnxn_cuda/./nbnxn_cuda_generated_nbnxn_cuda.cu.o
I read the report (http://redmine.gromacs.org/issues/1110)
and tried some combinations. This was my last failing
attempt:
- - - 8 - - - - - - - - - - - - - - - - - - - - - - - - - -
#!/bin/sh
export GMXVERSION=gromacs-4.6.3
export GMXTARGET=/opt/gromacs463
MINC=/opt/intel/mkl/include
On 25.07.2013 12:28, Mark Abraham wrote:
What doesn't work about the install guide instructions: 'Using MKL
with icc 11 or higher is very simple. Set up your compiler environment
correctly, perhaps with a command like source /path/to/compilervars.sh
intel64 (or consult your local documentation).
On 24.07.2013 04:08, Carlos Bueno wrote:
*Hi,*
*I keep getting errors when I try to install gromacs in OpenSuse 12.1.*
*I have installed cuda 5.0 and the nvidia cards. **I have tried with
different parameters for cmake:*
How did you install Cuda5? What did you install and how?
I have one
On 09.07.2013 16:11, Neha wrote:
I had a question about trjconv. After one of my simulations has ended I want
to use the final structure file to run some other simulations. However, what
I want to do is run an NVT run using the average box size of the earlier
run. Since the final structure file
On 22.06.2013 17:31, Mare Libero wrote:
I am assembling a GPU workstation to run MD simulations, and I was wondering if
anyone has any recommendation regarding the GPU/CPU combination.
From what I can see, the GTX690 could be the best bang for my buck in terms of
number of cores, memory,
On 22.06.2013 22:18, Mare Libero wrote:
The vendor I contacted was pushing for one of the
high end i7 processors with hyper-threading. But from what I can read,
most of the MD software don't make any use of it. So, using a the
multi-cores AMD (like your FX-8350) can be a cheaper and more
On 19.06.2013 15:25, Neha wrote:
Here's the full mdp file. Please let me know if you need anymore information
and thank you so much for helping!
dt = 0.02
Should be 0.03 according to S. Marrinks own remarks
(but wouldn't change your experience)
nstcomm
Addendum:
On 19.06.2013 23:16, Mirco Wahab wrote:
...
MARTINI W is a strongly associating fluid and will freeze
trough your box in no time even when setting negative pressure
below 300K. In newer Gromacs versions (from 4.6) there seems
to be additional shift (?) in the potential, so the water
On 08.06.2013 10:46, Bhamy Maithry Shenoy wrote:
Hi,
Thanks for your reply. But the problem still persists. Even now I am not able
to download.
Can you download from this link?
ftp://ftp.gromacs.org/pub/gromacs/
--
gmx-users mailing listgmx-users@gromacs.org
On 08.06.2013 14:39, Bhamy Maithry Shenoy wrote:
Can you download from this link?
ftp://ftp.gromacs.org/pub/gromacs/
I could not download from the mentioned link.
Then, your provider/router and/or your network
configuration is blocking FTP port traffic (Port 21),
but not HTTP port traffic
On 03.06.2013 18:43, Neha wrote:
I am a new user to Gromacs and am working on lipid simulations with the
Martini forcefield. The Martini website provides a pre-equilibrated DPPC
bilayer, and I was wondering if there were any told that would allow me to
convert this bilayer into a monolayer. For
On 28.05.2013 13:39, vidhya sankar wrote:
cmake .. -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs4.6 -DGMX_DOUBLE=ON
-DGMX_BINARY_SUFFIX=_d
please try
cmake .. -DGMX_CPU_ACCELERATION=SSE4.1
-DCMAKE_INSTALL_PREFIX=/usr/local/gromacs4.6 -DGMX_DOUBLE=ON
-DGMX_BINARY_SUFFIX=_d
I remember to have
On 28.05.2013 17:11, vidhya sankar wrote:
As you Mailed Me I have compiled gromacs 4.6
I have installed using the command As posted in mail
But I have AMD 8 Core black Edition
When I run the mdrun I saw a warning
Note: file tpx version 73, software tpx version 83
Using 8 MPI threads
Compiled
On 15.05.2013 06:41, Андрей Гончар wrote:
I know, but on target machine there is a gcc compilator version 4.1, and on
gromacs site they told that this version is broken and 4.5 should used
instead. So I try to compile it on machine with 4.5 version of gcc
Андрей, if there is *no fftw3f on the
On 02.05.2013 18:32, Albert wrote:
I've got a question about where can be obtain circled lipids bilayer?
like shown here:
http://wwwuser.gwdg.de/~ggroenh/membed/vesicle.png
As has already been said by others, this is not really a circled
lipid bilayer but rather a lipid vesicle of very very
On 12.04.2013 20:20, Szilárd Páll wrote:
On Fri, Apr 12, 2013 at 3:45 PM, 라지브간디 ra...@kaist.ac.kr wrote:
Can cygwin recognize the CUDA installed in win 7? if so, how do i link them ?
Good question, I've no idea whether it can as I myself have never
built GROMACS with CUDA on cygwin neither
On 01.04.2013 14:58, 라지브간디 wrote:
I tried to install 4.6.1 version through cygwin and got following error by
using this command :
In the last weeks of March 2013, there has been significant
progress made on the cygwin packages. Since April, 1st, there
is even a 64-bit build including gcc 4.8
On 13.03.2013 20:11, Mark Abraham wrote:
I think that post is saying you want
cmake -DCMAKE_INSTALL_PREFIX=/usr/local/lib -DGMX_GPU=OFF
-DGMX_BUILD_OWN_FFTW=OFF ../gromacs-4.6
and to make sure your PATH contains /usr/local/lib. I haven't tried it. I
don't know whether source-ing GMXRC in the
On 13.03.2013 19:31, neshat haq wrote:
It would be great help please elaborate the steps.
I am installing the gromacs-4.6 on my desktop mostly for the analysis
purpose.
Neshat, if you have x64 windows machine, I'd recommend to build
a windows-64-version of Gromacs. You can do this with the
Am 11.12.2012 16:04, schrieb Szilárd Páll:
It looks like some gcc 4.7-s don't work with CUDA, although I've been using
various Ubuntu/Linaro versions, most recently 4.7.2 and had no
issues whatsoever. Some people seem to have bumped into the same problem
(see http://goo.gl/1onBz or
Hello Peter,
Am 02.05.2012 17:44, schrieb Peter C. Lai:
You can wait for ivy bridge, then stick some Kepler GPUs (nvidia gtx
680) in it. That should max the performance. asm is pretty much stagnant
for general purpose procs since core2 came out.
Is this true?
To my knowledge, the Fermi GPU
On 18.01.2012 07:31, Ravi Kumar Venkatraman wrote:
Dear All,
I have ran a 10 ns production run for chloranil in 500 methanol solvent box. I
want to get the coordinates of solvent and solute at different time steps from
the trajectory file (*.xtc). Can anybody tell me how to extract the details
For checking the id of the last frame contained
in a trajectory, I usually apply ugly command line
hacks like:
echo 0|trjconv -dump 1e10 -o /tmp/x.gro 21/dev/null|perl -lne 'print $1
if /t=(\d+)$/'
which might look awe-inspiring first but is of course tiresome.
Did I overlook the appropriate
On 13.11.2011 02:10, Mirco Wahab wrote:
I was able to build Gromacs 4.5.5 (32 bit) on Cygwin (gcc 4.5.3)
w/o threads
For a better understanding of the usability of
cygwin-compiled Gromacs under windows I performed
some more tests on my desktop box.
First, I tried to install recent versions
On 10.11.2011 15:28, Szilárd Páll wrote:
On Tue, Nov 8, 2011 at 11:59 PM, Mark Abrahammark.abra...@anu.edu.auwrote:
Actually I don't think this issue has been addressed. Some NUMA-aware
thread_mpi stuff does not work under Cygwin, and code added since 4.5.4
assumes that it does. I can find no
On 02.11.2011 13:38, Ravi Kumar Venkatraman wrote:
Could anybody suggest me some books or notes or some
materials which will help me to understand the way gromacs algorithms work
i.e. how neighbor group search works e.t.c. I kindly request you to suggest
me other than the gromacs manual.*
On 24.10.2011 23:23, Szilárd Páll wrote:
I've just realized that both you and the similar report you linked to
were using CMake 2.8.3. If you don't succeed could you try another
CMake version?
I could replicate the error with the simple cmake inviocation you proposed in
your reply:
cmake
On 17.10.2011 05:18, Mark Abraham wrote:
On 17/10/2011 7:04 AM, Mirco Wahab wrote:
On 10/16/2011 2:25 PM, Mark Abraham wrote:
On 15/10/2011 9:02 PM, Mirco Wahab wrote:
On 10/15/2011 1:15 AM, Mark Abraham wrote:
I use
...
...
...
OK, I can understand that. But if the options (-mtune
On 10/16/2011 2:25 PM, Mark Abraham wrote:
On 15/10/2011 9:02 PM, Mirco Wahab wrote:
On 10/15/2011 1:15 AM, Mark Abraham wrote:
I use
...
...
//Flags used by the compiler during all build types
CMAKE_CXX_FLAGS:STRING=' -msse2 -ip -funroll-all-loops -std=gnu99 '
//Flags used by the compiler
On 10/16/2011 10:04 PM, Mirco Wahab wrote:
- gcc 4.5.1 x64 (Linux) (20101208)
with the said gcc, all builds works fine, the problem
arises with the Intel suite (icc/icpc 12.1.0)
sorry for the typo.
M.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman
On 10/15/2011 1:15 AM, Mark Abraham wrote:
I use
ccmake ..\
-DGMX_FFT_LIBRARY=mkl \
-DMKL_LIBRARIES=${MKL}/lib/em64t/libmkl_intel_thread.so;${MKL}/lib/em64t/libmkl_lapack.so;${MKL}/lib/em64t/libmkl_core.so;${MKL}/lib/em64t/libmkl_em64t.a;${MKL}/lib/em64t/libguide.so;/usr/lib64/libpthread.so
\
Dear Gromacs users,
I'm trying to build an Intel-MKL-linked version of
gromacs 4.5.5 and can't figure how to do that using
cmake.
There are already some (new) instructions on the GROMACS
web site regarding Intel icc but not how to use the
corresponding mkl.
On my system, the Intel 2011 (non
I will be installing gromacs 4.5.x in another computer but this time with four
cores. The PC runs in windows and I will be using cygwin.
... Do I still need to install MPI using cygwin?
Probably not, but I haven't tested threading on Cygwin.
I just did a test for fun and it worked remarkably
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