Re: [gmx-users] energy drift - comparison of double and single precision
Could you try to reduce the nstcalcenergy flag from 100 to 10 and then one? Similar flags apply to temperature and pressure and I believe might seriously affect energy conservation. XAvier. On Oct 12, 2013, at 0:50, Mark Abraham mark.j.abra...@gmail.com wrote: Didn't see any problem in the .mdp. -4500 kJ/mol in 10ns over (guessing) 30K atoms is 0.015 kJ/mol/ns/atom. k_B T is at least 100 times larger than that. I bet the rest of the lysozyme model physics is not accurate to less than 1% ;-) There are some comparative numbers at http://dx.doi.org/10.1016/j.cpc.2013.06.003 - the two systems are rather different but they share the use of SETTLE. Note that using md-vv guarantees the 2007 paper is inapplicable, because GROMACS did not have a velocity Verlet integrator back then. Sharing the .log files might be informative. Mark On Fri, Oct 11, 2013 at 11:38 PM, Guillaume Chevrot guillaume.chev...@gmail.com wrote: Hi, sorry for my last post! I re-write my e-mail (with some additional information) and I provide the links to my files ;-) I compared the total energy of 2 simulations: lysozyme in water / NVE ensemble / single precision / Gromacs 4.6.3 lysozyme in water / NVE ensemble / double precision / Gromacs 4.6.3 ... and what I found was quite ... disturbing (see the plots of the total energy: http://dx.doi.org/10.6084/m9.figshare.820153). I observe a constant drift in energy in the case of the single precision simulation. Did I do something wrong*? Any remarks are welcomed! Here is the link to the ‘mdout.mdp’ file (http://dx.doi.org/10.6084/m9.figshare.820154) so you can check what mdp options I used. My second question is: if I did not do something wrong, what are the consequences on the simulation? Can I trust the results of single precision simulations? Regards, Guillaume *PS: I am not the only one encountering this behavior. In the literature, this problem has already been mentioned: http://jcp.aip.org/resource/1/jcpsa6/v126/i4/p046101_s1 2013/10/11 Mark Abraham mark.j.abra...@gmail.com On Oct 11, 2013 7:59 PM, Guillaume Chevrot guillaume.chev...@gmail.com wrote: Hi all, I recently compared the total energy of 2 simulations: lysozyme in water / NVE ensemble / single precision lysozyme in water / NVE ensemble / double precision ... and what I found was quite ... disturbing (see the attached figure - plots of the total energy). I observe a constant drift in energy in the case of the single precision simulation. Did I do something wrong*? Any remarks are welcomed! I join the ‘mdout.mdp’ file so you can check what mdp options I used. Maybe. Unfortunately we cannot configure the mailing list to allow people to send attachments to thousands of people, so you will need to do something like provide links to files on a sharing service. My second question is: if I did not do something wrong, what are the consequences on the simulation? Can I trust the results of single precision simulations? Yes, as you have no doubt read in the papers published by the GROMACS team. Regards, Guillaume *PS: I am not the only one encountering this behavior. In the literature, this problem has already been mentioned: http://jcp.aip.org/resource/1/jcpsa6/v126/i4/p046101_s1 ... which is six years old, examining the properties of code seven years old. Life has moved on! :-) Even if you have found a problem, it is a big assumption that this is (still) the cause. Mark -- 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 the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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 the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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 the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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.
Re: [gmx-users] energy drift - comparison of double and single precision
2013/10/12 Mark Abraham mark.j.abra...@gmail.com Didn't see any problem in the .mdp. -4500 kJ/mol in 10ns over (guessing) 30K atoms is 0.015 kJ/mol/ns/atom. k_B T is at least 100 times larger than that. I bet the rest of the lysozyme model physics is not accurate to less than 1% ;-) There are some comparative numbers at http://dx.doi.org/10.1016/j.cpc.2013.06.003 - the two systems are rather different but they share the use of SETTLE. Do you suggest that SETTLE is the cause of the drift? (note: If I did not mistaken, my drift would be 0.18 [k_B T / ns / atom], quite close of the figures shown in their figure 2.) In their Figure 2, they show a drift for single and double precision, and it is not the case for my double precision simulation, so maybe SETTLE is no the cause of my trouble? Note that using md-vv guarantees the 2007 paper is inapplicable, because GROMACS did not have a velocity Verlet integrator back then. Sharing the If I remember well, their demonstration was true whatever the integrator. Nevertheless, I also tested the leap-frog integrator, and I observe the same drift in energy. So maybe their explanation is still applicable. .log files might be informative. Here is the link where you can find the log file: http://dx.doi.org/10.6084/m9.figshare.821211 Thanks for your comments! Guillaume Mark On Fri, Oct 11, 2013 at 11:38 PM, Guillaume Chevrot guillaume.chev...@gmail.com wrote: Hi, sorry for my last post! I re-write my e-mail (with some additional information) and I provide the links to my files ;-) I compared the total energy of 2 simulations: lysozyme in water / NVE ensemble / single precision / Gromacs 4.6.3 lysozyme in water / NVE ensemble / double precision / Gromacs 4.6.3 ... and what I found was quite ... disturbing (see the plots of the total energy: http://dx.doi.org/10.6084/m9.figshare.820153). I observe a constant drift in energy in the case of the single precision simulation. Did I do something wrong*? Any remarks are welcomed! Here is the link to the ‘mdout.mdp’ file (http://dx.doi.org/10.6084/m9.figshare.820154) so you can check what mdp options I used. My second question is: if I did not do something wrong, what are the consequences on the simulation? Can I trust the results of single precision simulations? Regards, Guillaume *PS: I am not the only one encountering this behavior. In the literature, this problem has already been mentioned: http://jcp.aip.org/resource/1/jcpsa6/v126/i4/p046101_s1 2013/10/11 Mark Abraham mark.j.abra...@gmail.com On Oct 11, 2013 7:59 PM, Guillaume Chevrot guillaume.chev...@gmail.com wrote: Hi all, I recently compared the total energy of 2 simulations: lysozyme in water / NVE ensemble / single precision lysozyme in water / NVE ensemble / double precision ... and what I found was quite ... disturbing (see the attached figure - plots of the total energy). I observe a constant drift in energy in the case of the single precision simulation. Did I do something wrong*? Any remarks are welcomed! I join the ‘mdout.mdp’ file so you can check what mdp options I used. Maybe. Unfortunately we cannot configure the mailing list to allow people to send attachments to thousands of people, so you will need to do something like provide links to files on a sharing service. My second question is: if I did not do something wrong, what are the consequences on the simulation? Can I trust the results of single precision simulations? Yes, as you have no doubt read in the papers published by the GROMACS team. Regards, Guillaume *PS: I am not the only one encountering this behavior. In the literature, this problem has already been mentioned: http://jcp.aip.org/resource/1/jcpsa6/v126/i4/p046101_s1 ... which is six years old, examining the properties of code seven years old. Life has moved on! :-) Even if you have found a problem, it is a big assumption that this is (still) the cause. Mark -- 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 the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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 the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] energy drift - comparison of double and single precision
2013/10/12 XAvier Periole x.peri...@rug.nl Could you try to reduce the nstcalcenergy flag from 100 to 10 and then one? Thanks for the suggestion. I'll try next week and I'll show the results ASAP. Guillaume Similar flags apply to temperature and pressure and I believe might seriously affect energy conservation. XAvier. On Oct 12, 2013, at 0:50, Mark Abraham mark.j.abra...@gmail.com wrote: Didn't see any problem in the .mdp. -4500 kJ/mol in 10ns over (guessing) 30K atoms is 0.015 kJ/mol/ns/atom. k_B T is at least 100 times larger than that. I bet the rest of the lysozyme model physics is not accurate to less than 1% ;-) There are some comparative numbers at http://dx.doi.org/10.1016/j.cpc.2013.06.003 - the two systems are rather different but they share the use of SETTLE. Note that using md-vv guarantees the 2007 paper is inapplicable, because GROMACS did not have a velocity Verlet integrator back then. Sharing the .log files might be informative. Mark On Fri, Oct 11, 2013 at 11:38 PM, Guillaume Chevrot guillaume.chev...@gmail.com wrote: Hi, sorry for my last post! I re-write my e-mail (with some additional information) and I provide the links to my files ;-) I compared the total energy of 2 simulations: lysozyme in water / NVE ensemble / single precision / Gromacs 4.6.3 lysozyme in water / NVE ensemble / double precision / Gromacs 4.6.3 ... and what I found was quite ... disturbing (see the plots of the total energy: http://dx.doi.org/10.6084/m9.figshare.820153). I observe a constant drift in energy in the case of the single precision simulation. Did I do something wrong*? Any remarks are welcomed! Here is the link to the ‘mdout.mdp’ file (http://dx.doi.org/10.6084/m9.figshare.820154) so you can check what mdp options I used. My second question is: if I did not do something wrong, what are the consequences on the simulation? Can I trust the results of single precision simulations? Regards, Guillaume *PS: I am not the only one encountering this behavior. In the literature, this problem has already been mentioned: http://jcp.aip.org/resource/1/jcpsa6/v126/i4/p046101_s1 2013/10/11 Mark Abraham mark.j.abra...@gmail.com On Oct 11, 2013 7:59 PM, Guillaume Chevrot guillaume.chev...@gmail.com wrote: Hi all, I recently compared the total energy of 2 simulations: lysozyme in water / NVE ensemble / single precision lysozyme in water / NVE ensemble / double precision ... and what I found was quite ... disturbing (see the attached figure - plots of the total energy). I observe a constant drift in energy in the case of the single precision simulation. Did I do something wrong*? Any remarks are welcomed! I join the ‘mdout.mdp’ file so you can check what mdp options I used. Maybe. Unfortunately we cannot configure the mailing list to allow people to send attachments to thousands of people, so you will need to do something like provide links to files on a sharing service. My second question is: if I did not do something wrong, what are the consequences on the simulation? Can I trust the results of single precision simulations? Yes, as you have no doubt read in the papers published by the GROMACS team. Regards, Guillaume *PS: I am not the only one encountering this behavior. In the literature, this problem has already been mentioned: http://jcp.aip.org/resource/1/jcpsa6/v126/i4/p046101_s1 ... which is six years old, examining the properties of code seven years old. Life has moved on! :-) Even if you have found a problem, it is a big assumption that this is (still) the cause. Mark -- 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 the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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 the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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 the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing
[gmx-users] DSSP problem
Dear users; I am trying to run DSSP and have problem, I typed in terminal do_dssp -f bLac_orig_md2.trr -s bLac_orig_md2.tpr -sc Secondary_Structure_analysis_original_dss.xvg -ssdump and got the following error, Program do_dssp, VERSION 4.6.3 Source code file: /home/mass/gromacs-4.6.3/src/gmxlib/gmxfio.c, line: 524 Can not open file: bLac_orig_md2.trr For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I can see the file bLac_orig_md2.trr in the directory any comments? -- 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 the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] DSSP problem
On 10/12/13 6:08 PM, Mass wrote: Dear users; I am trying to run DSSP and have problem, I typed in terminal do_dssp -f bLac_orig_md2.trr -s bLac_orig_md2.tpr -sc Secondary_Structure_analysis_original_dss.xvg -ssdump and got the following error, Program do_dssp, VERSION 4.6.3 Source code file: /home/mass/gromacs-4.6.3/src/gmxlib/gmxfio.c, line: 524 Can not open file: bLac_orig_md2.trr For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I can see the file bLac_orig_md2.trr in the directory any comments? Please provide the copied and pasted output of ls -l in that directory. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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 the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Gromacs on Stampede
Hello,
I have a question about running gromacs utilities on Stampede and hopefully
someone can point me in the right direction. I compiled gromacs using
instructions in this thread and mdrun works fine. Also, some utilities like
g_energy, g_analyze (single - core utilities, I believe) seem to be working
fine.
I am interested in computing life time of hydrogen bonds and this calculation
is quite expensive. Is there a way to submit this as a job using 32 or higher
cores? When I run g_hbond on my workstation (16 cores) it runs on 16 threads by
default. However, I am not sure if it is a good idea to run it on Stampede
without submitting it as a job.
I noticed that g_hbond works on OpenMP, while gromacs was compiled for Mpi
according to these instructions. Just curious, if that would be the reason and
if there is a suitable workaround for this problem.
As always, help is greatly appreciated.
Thanks,
On Friday, October 11, 2013 5:31 AM, Arun Sharma arunsharma_...@yahoo.com
wrote:
Dear Chris,
Thank you so much for providing the scripts and such detailed instructions. I
was trying to load the gromacs module that is already available and was unable
to get it to run.
Thanks to you, I now have a working gromacs installation.
On Thursday, October 10, 2013 2:59 PM, Christopher Neale
chris.ne...@mail.utoronto.ca wrote:
Dear Arun:
here is how I compile fftw and gromacs on stampede.
I have also included a job script and a script to submit a chain of jobs.
As Szilárd notes, this does not use the MICs, but it is still a rather fast
machine.
# Compilation for single precision gromacs plus mdrun_mpi
#
# Compile fftw on stampede:
cd fftw-3.3.3
mkdir exec
export FFTW_LOCATION=$(pwd)/exec
module purge
module load intel/13.0.2.146
export CC=icc
export CXX=icpc
./configure --enable-float --enable-threads --prefix=${FFTW_LOCATION}
--enable-sse2
make -j4
make -j4 install
cd ../
# Compile gromacs 4.6.1 on stampede:
cd gromacs-4.6.1
mkdir source
mv * source
mkdir exec
cd exec
module purge
module load intel/13.0.2.146
module load cmake/2.8.9
export FFTW_LOCATION=$(pwd)/../fftw-3.3.3/exec
export CXX=icpc
export CC=icc
cmake ../source/ \
-DCMAKE_PREFIX_PATH=$FFTW_LOCATION \
-DCMAKE_INSTALL_PREFIX=$(pwd) \
-DGMX_X11=OFF \
-DCMAKE_CXX_COMPILER=${CXX} \
-DCMAKE_C_COMPILER=${CC} \
-DGMX_PREFER_STATIC_LIBS=ON \
-DGMX_MPI=OFF
make -j4
make -j4 install
cd ../
mkdir exec2
cd exec2
module purge
module load intel/13.0.2.146
module load cmake/2.8.9
module load mvapich2/1.9a2
export FFTW_LOCATION=$(pwd)/../fftw-3.3.3/exec
export CXX=mpicxx
export CC=mpicc
cmake ../source/ \
-DCMAKE_PREFIX_PATH=$FFTW_LOCATION \
-DCMAKE_INSTALL_PREFIX=$(pwd) \
-DGMX_X11=OFF \
-DCMAKE_CXX_COMPILER=${CXX} \
-DCMAKE_C_COMPILER=${CC} \
-DGMX_PREFER_STATIC_LIBS=ON \
-DGMX_MPI=ON
make -j4 mdrun
make -j4 install-mdrun
cp bin/mdrun_mpi ../exec/bin
cd ../
# Here is a script that you can submit to run gromacs on stampede:
# Set SBATCH -A according to your allocation
# Set SBATCH -N to number of nodes
# Set SBATCH -n to number of nodes x 16 (= number of CPU cores)
# Set PATH and GMXLIB according to your compilation of gromacs
# Remove -notunepme option if you don't mind some of the new optimizations
#!/bin/bash
#SBATCH -J test # Job name
#SBATCH -o myjob.%j.out # Name of stdout output file (%j expands to jobId)
#SBATCH -p normal # Queue name
#SBATCH -N 7 # Total number of nodes requested (16
cores/node)
#SBATCH -n 112 # Total number of mpi tasks requested
#SBATCH -t 48:00:00 # Run time (hh:mm:ss)
#SBATCH -A TG-XX # -- Allocation name to charge job against
PATH=/home1/02417/cneale/exe/gromacs-4.6.1/exec/bin:$PATH
GMXLIB=/home1/02417/cneale/exe/gromacs-4.6.1/exec/share/gromacs/top
# grompp -f md.mdp -p new.top -c crashframe.gro -o md3.tpr -r restr.gro
ibrun mdrun_mpi -notunepme -deffnm md3 -dlb yes -npme 16 -cpt 60 -cpi md3.cpt
-nsteps 50 -maxh 47.9 -noappend
cp md3.cpt backup_md3_$(date|sed s/ /_/g).cpt
# submit the above script like this:
sbatch script.sh
# or create a chain of jobs like this:
N=8
script=stamp.sh
if [ ! -e last_job_in_chain ]; then
id=$(sbatch ${script}|tail -n 1 |awk '{print $NF}')
echo $id last_job_in_chain
let N--
fi
id=$(cat last_job_in_chain)
for((i=1;i=N;i++)); do
id=$(sbatch -d afterany:${id} ${script}|tail -n 1 |awk
[gmx-users] Iron(III)Hydroxide complexing with Enterobactin (quantum chemistry calculations?)
Hello everybody, I am sorry to do this, but I only have knowledge in ochem (haven't taken pchem yet) so reading Car-Parrinello Molecular Dynamics and searching it on wikipedia yields no data that I understand. So what I'll do to save everyone time is to share what I want to do and ask if this software can do it, and if not, do you know of any software that can do this? My goal is to simulate Iron(III)Hydroxide in a box of water (perhaps physiological conditions/ions) with Enterobactin, to see if it will form an iron complex. Perhaps this is more for a quantum chemistry program? Any that you would suggest to use? Thank you for your time. -Jonathan Saboury -- 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 the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
