Dear all,
Here is a part of the *.mdp file I am using in coarse-grained
parametrization (Iterative Boltzmann Inversion method) of a molecule by
votca.
integrator = sd
tinit= 0
dt = 0.2
nsteps = 5000
init_step
Unfortunately using your shortened cmake args, I still get fpic errors. But it
does complete the build statically with -DGMX_BUILD_SHARED_EXE=OFF
CC=cc CXX=CC cmake ../ -DGMX_SIMD=AVX2_256 -DGMX_MPI=ON -DGMX_GPU=ON
-DCMAKE_PREFIX_PATH=${FFTW_DIR}/..
/usr/bin/ld:
CMakeFiles/libgromacs.dir/mdlib
Hello all,
I'm tuning MDrun on a node with 24 intel skylake cores (2X12) and 2 V100
GPUs. MPI-enabled (no thread-mpi) Gromacs 2018 ("2018.0") is compiled with
GCC, CUDA, OpenMPI, and OpenBLAS. I am trying to assign the two GPUs to
four ranks. My run command is:
mpirun -np 4 mdrun_mpi_s_g -ntomp 6
On CSCS Piz Daint I use the following command line (assuming
PrgEnv-gnu) where everything in "[]" is optional and compilation
should work just fine without.
CC=cc CXX=CC cmake ../
-DGMX_SIMD=THE_RIGHT_SIMD_FLAVOR
-DGMX_MPI=ON
-DGMX_GPU=ON
-DCMAKE_PREFIX_PATH=${FFTW_DIR}/.. \
[ -DGMX_FFT_LIBRARY=ff
Hi,
I am trying to select particles that are z < 20 and z > 10 as a function of
time.
I think I used gmx select correctly and generated an index file with group
names like "(z_<_.8_f2882_t23056.000)"
Now I am unsure how I use this index file for gmx trjconv or gmx density.
Does anybody have some
You are trying to give me a hint. :) My cmake args are taken from a co-worker,
and the statement syntax is from the CMakeCache.txt file. On a Cray you force
cc/CC and all the module libraries/headers should be automatically found.
Strangely it didn’t find fftw without help. Regardless I get the
Dear users,
I would like to use the constant velocities for all the atoms of both protein
and ligand during all the simulation steps (EM, NVT, NPT and MD). Do you know
how I can do that with GROMACS? In this case, the COM, the linear momentum and
angular momentum of both groups wouldn't change
FYI: not even a my vanilla (non-CRAY) local build which does work
otherwise succeeds with
cmake . -DCUDA_NVCC_FLAGS:STRING="-rdc=true"
so as I guessed, that's the culprit.
Out of curiosity I wonder: what's the reason for the "inventive" use
of CMake options, none of which are needed?
--
Szilárd
I think the fpic errors can't be caused by missing rdc=true because
the latter refers to the GPU _device_ code, but GROMACS does not need
relocatable device code, so that should not be necessary.
--
Szilárd
On Fri, Apr 6, 2018 at 6:33 PM, Borchert, Christopher B
ERDC-RDE-ITL-MS Contractor
wrote:
Thanks Szilárd. My understanding is rdc is nvcc's equivalent of fpic. I get
fpic errors without it. In fact I get fpic errors without including fpic
explicitly in the C/CXX flags.
/usr/bin/ld:
CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_cuda.cu.o:
relocation R_X86_64_
Also, can the "map file format" page be updated with "chain separator"?
http://manual.gromacs.org/online/map.html
9
~ Coil 1 1 1
E B-Sheet 1 0 0
B B-Bridge 0 0 0
I went on to refresh my memory a bit and I thought I'd share a summary
for those curious.
The actual clocks CPU will be running at are determined by a number of
factors: base and boost clocks (by spec), actual boost clocks
achievable (depending on cores used, workload, TDP) and this is not
hugely
I know the paper but the webpage
Thanks you Viveca
--
Message: 2
Date: Fri, 6 Apr 2018 16:45:45 +0200
From: Viveca Lindahl
To: gmx-us...@gromacs.org
Cc: "gromacs.org_gmx-users@maillist.sys.kth.se"
Subject: Re: [gmx-users] Speed up simulations with GROMACS w
Hi,
What is the reason for using the custom CMake options? What's the
-rdc=true for -- I don't think it's needed and it can very well be
causing the issue. Have you tried to actually do an
as-vanilla-as-possible build?
--
Szilárd
On Thu, Apr 5, 2018 at 6:52 PM, Borchert, Christopher B
ERDC-RDE-
Hi,
There is this ancient gromacs page which I guess you already found:
http://www.gromacs.org/Documentation/How-tos/Removing_fastest_degrees_of_freedom
Here are a couple of references, the second for using virtual sites for
CHARMM lipids:
Bjelkmar, P., Larsson, P., Cuendet, M. A., Hess, B. & Li
I would like to share my answer for chain separator issue for the "gmx
do_dssp". Millions of thanks to Carsten!
The "gmx do_dssp" will output an additional line as chain separator between two
chains. We do NOT need to provide a "ss.map" file in our working directory, and
the command will find
Use google the "site:" keyword is ideal for that.
--
Szilárd
On Fri, Apr 6, 2018 at 3:51 PM, ZHANG Cheng <272699...@qq.com> wrote:
> Dear Gromacs,
> I know I can see all the post from
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/
>
>
> but can I search from this link? I do not w
Dear Gromacs,
I know I can see all the post from
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/
but can I search from this link? I do not want to download all of them to my PC.
Thank you.
Yours sincerely
Cheng
--
Gromacs Users mailing list
* Please search the archive at
http
Hi Stephane,
I hope it is useful. I am afraid I have very little charmm experience. I used
the approach posted for an amber ff. I hope someone can help with the charmm
aspect.
Kind regards
Anthony Nash PhD MRSC
Department of Physiology, Anatomy, and Genetics
University of Oxford
Many thanks Anthony
I will read your post blog. I have another quick question: Does the approach
work by defaults (w/o modifications) for other biomolecules such as surfactants
or it is necessary to construct a virtual site table as we can found for
protein in the charmm*.ff distribution ?
St
Hi,
I tried something like this about a year ago and I put an instructional blog
post together. Warning: it was pulled together from a paper I found and not my
own efforts although I did get it to work. Any questions I might not be able to
respond, I'm on vacation!
https://distributedscience.
Hi gmx users,
I know that it is possible to speed up the simulations by a factor 2 (by using
a larger timestep) in GROMACS with virtual interaction sites. By I do not find
a clear procedure on the web in particular if I use CHARMM. Do you have any
pointers or procedures and examples of mdp fi
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