Re: [gmx-users] Gromacs on Stampede
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 '{print $NF}')
echo $id last_job_in_chain
done
--
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Re: [gmx-users] DSSP installation on Ubuntu 12.10
On 10/11/13 1:34 AM, Mass wrote: Dear Mark, Thanks for your comments, I uninstalled my previous Gromacs version ( from Ubuntu software centre I just removed it) . and followed the dirty and quick installation on Gromacs website tar xfz gromacs-4.6.3.tar.gz cd gromacs-4.6.3 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON make sudo make install source /usr/local/gromacs/bin/GMXRC I have one question here, why when I run mdrun in my home directory it is telling me that Gromacs is not installed, but when I source it again and go to my home directory after that mdrun show Gromacs version-4.6.3. any comments on this? how can I call gromacs without sourcing every time Configure your login scripts to do it for you. secondly when I do do_dssp do_dssp -f bLac_orig_md2.trr -s bLac_orig_md2.tpr -sc Secondary_Structure_analysis_original_dss.xvg -ssdump I am getting following error Program mdrun, VERSION 4.6.3 Source code file: /home/mass/gromacs-4.6.3/src/gmxlib/gmxfio.c, line: 524 Can not open file: topol.tpr For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Whatever you typed above is not what you typed in the terminal (always copy and paste!), because do_dssp is looking for topol.tpr, which is the default name for -s. If you do not specify a particular required input, all Gromacs programs look for default names. -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] DSSP installation on Ubuntu 12.10
Hi Justin, Sorry for the mistake, 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? On Saturday, October 12, 2013 12:55 AM, Justin Lemkul jalem...@vt.edu wrote: On 10/11/13 1:34 AM, Mass wrote: Dear Mark, Thanks for your comments, I uninstalled my previous Gromacs version ( from Ubuntu software centre I just removed it) . and followed the dirty and quick installation on Gromacs website tar xfz gromacs-4.6.3.tar.gz cd gromacs-4.6.3 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON make sudo make install source /usr/local/gromacs/bin/GMXRC I have one question here, why when I run mdrun in my home directory it is telling me that Gromacs is not installed, but when I source it again and go to my home directory after that mdrun show Gromacs version-4.6.3. any comments on this? how can I call gromacs without sourcing every time Configure your login scripts to do it for you. secondly when I do do_dssp do_dssp -f bLac_orig_md2.trr -s bLac_orig_md2.tpr -sc Secondary_Structure_analysis_original_dss.xvg -ssdump I am getting following error Program mdrun, VERSION 4.6.3 Source code file: /home/mass/gromacs-4.6.3/src/gmxlib/gmxfio.c, line: 524 Can not open file: topol.tpr For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Whatever you typed above is not what you typed in the terminal (always copy and paste!), because do_dssp is looking for topol.tpr, which is the default name for -s. If you do not specify a particular required input, all Gromacs programs look for default names. -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] DSSP installation on Ubuntu 12.10
On 10/11/13 8:12 AM, Mass wrote: Hi Justin, Sorry for the mistake, 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? Check for typos. If the file is actually there, has the right permissions (readable), and has that name, it is impossible to trigger the fatal error. -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] DSSP installation on Ubuntu 12.10
Dear Gromacs user, Can anyone tell me how to arrange for my login scripts to source gromacs automatically? Justin just point that to me and in Gromacs website it is written search the web for that, anyone know how to do that? Thanks On Saturday, October 12, 2013 1:12 AM, Mass masstransfer_2...@yahoo.com wrote: Hi Justin, Sorry for the mistake, 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? On Saturday, October 12, 2013 12:55 AM, Justin Lemkul jalem...@vt.edu wrote: On 10/11/13 1:34 AM, Mass wrote: Dear Mark, Thanks for your comments, I uninstalled my previous Gromacs version ( from Ubuntu software centre I just removed it) . and followed the dirty and quick installation on Gromacs website tar xfz gromacs-4.6.3.tar.gz cd gromacs-4.6.3 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON make sudo make install source /usr/local/gromacs/bin/GMXRC I have one question here, why when I run mdrun in my home directory it is telling me that Gromacs is not installed, but when I source it again and go to my home directory after that mdrun show Gromacs version-4.6.3. any comments on this? how can I call gromacs without sourcing every time Configure your login scripts to do it for you. secondly when I do do_dssp do_dssp -f bLac_orig_md2.trr -s bLac_orig_md2.tpr -sc Secondary_Structure_analysis_original_dss.xvg -ssdump I am getting following error Program mdrun, VERSION 4.6.3 Source code file: /home/mass/gromacs-4.6.3/src/gmxlib/gmxfio.c, line: 524 Can not open file: topol.tpr For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Whatever you typed above is not what you typed in the terminal (always copy and paste!), because do_dssp is looking for topol.tpr, which is the default name for -s. If you do not specify a particular required input, all Gromacs programs look for default names. -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] DSSP installation on Ubuntu 12.10
On 10/11/13 8:57 AM, Mass wrote: Dear Gromacs user, Can anyone tell me how to arrange for my login scripts to source gromacs automatically? Justin just point that to me and in Gromacs website it is written search the web for that, anyone know how to do that? It depends on your shell. In bash, you can just add the line that sources GMXRC to .bashrc. -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] DSSP installation on Ubuntu 12.10
Maintaining your login scripts is a basic UNIX issue, not a GROMACS issue. Google knows a lot more about it than anybody here ;-) Mark On Fri, Oct 11, 2013 at 2:57 PM, Mass masstransfer_2...@yahoo.com wrote: Dear Gromacs user, Can anyone tell me how to arrange for my login scripts to source gromacs automatically? Justin just point that to me and in Gromacs website it is written search the web for that, anyone know how to do that? Thanks On Saturday, October 12, 2013 1:12 AM, Mass masstransfer_2...@yahoo.com wrote: Hi Justin, Sorry for the mistake, 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? On Saturday, October 12, 2013 12:55 AM, Justin Lemkul jalem...@vt.edu wrote: On 10/11/13 1:34 AM, Mass wrote: Dear Mark, Thanks for your comments, I uninstalled my previous Gromacs version ( from Ubuntu software centre I just removed it) . and followed the dirty and quick installation on Gromacs website tar xfz gromacs-4.6.3.tar.gz cd gromacs-4.6.3 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON make sudo make install source /usr/local/gromacs/bin/GMXRC I have one question here, why when I run mdrun in my home directory it is telling me that Gromacs is not installed, but when I source it again and go to my home directory after that mdrun show Gromacs version-4.6.3. any comments on this? how can I call gromacs without sourcing every time Configure your login scripts to do it for you. secondly when I do do_dssp do_dssp -f bLac_orig_md2.trr -s bLac_orig_md2.tpr -sc Secondary_Structure_analysis_original_dss.xvg -ssdump I am getting following error Program mdrun, VERSION 4.6.3 Source code file: /home/mass/gromacs-4.6.3/src/gmxlib/gmxfio.c, line: 524 Can not open file: topol.tpr For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Whatever you typed above is not what you typed in the terminal (always copy and paste!), because do_dssp is looking for topol.tpr, which is the default name for -s. If you do not specify a particular required input, all Gromacs programs look for default names. -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 -- 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] Building lipid bilayers topology
Hi everyone. I am a relatively new user of GROMACS having recently needed to carry out research on proteins aggregation. I am currently building a DMPC/DMPG 1:1 membrane by assembling individual DMPC and DMPG lipid molecules and then using genconf to generate the amount of lipids needed. The DMPC topology was taken from Dr. Tielman website, while DMPG was taken from lipidbook. Now I am facing issue as to how to I make the topologies for the 2 different lipids compatible with each other. The DMPC topology is compatible with gromos combined with Berger lipid parameter, while the DMPG was done with 54A7. I would like to use 54A7 without Berger lipid parameters, what would be the best way to do it? Modifying the residue name? If so, do I only have to modify the topology dmpc.itp that comes from Dr. Tielman website, such that the residue name follows the 54A7 convention? The reason I want to use the lipid without Berger lipid is that there's a recent paper http://pubs.acs.org/doi/abs/10.1021/ct300675z that suggests that 54A7 is the better united atom FF as compared to the other FF commonly used, including the Berger Gromos combination. What is your opinion? Best Regards, Khi Pin -- View this message in context: http://gromacs.5086.x6.nabble.com/Building-lipid-bilayers-topology-tp5011774.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] bonded interactions in Gromos96
Hi gromacs users, I tried to add new bonded interactions to the ffbonded.itp file in gromos96, but I am confused about the used parameters in the descriptions. Here is an example: #define gb_10.1000 1.5700e+07 ; H - OA 750 The equation used in gromos is Vb(r_ij)=(1/4) k_ij (r_ij^2 - b_ij^2)^2 I see two unknowns: k_ij and b_ij; but there are 3 numbers in the definition: 0.1000, 1.5700e+07, 750. The same story for the angle potential: #define ga_1 90.00 380.00 ; NR(heme) - FE - C 90 The equation used in gromos is Va(theta_ijk)=(1/2) k_ijk (cos(theta_ijk) - cos(theta0_ijk))^2 I see two unknowns: k_ijk and theta0_ijk; but there are 3 numbers in the definition: 90.00, 380, 90. I appreciate if somebody could clarify this for me. Ehsan -- 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] Building lipid bilayers topology
On 10/11/13 12:24 PM, superpc wrote: Hi everyone. I am a relatively new user of GROMACS having recently needed to carry out research on proteins aggregation. I am currently building a DMPC/DMPG 1:1 membrane by assembling individual DMPC and DMPG lipid molecules and then using genconf to generate the amount of lipids needed. The DMPC topology was taken from Dr. Tielman website, while DMPG was taken from lipidbook. Now I am facing issue as to how to I make the topologies for the 2 different lipids compatible with each other. The DMPC topology is compatible with gromos combined with Berger lipid parameter, while the DMPG was done with 54A7. I would like to use 54A7 without Berger lipid parameters, what would be the best way to do it? Modifying the residue name? If so, do I only have to modify the topology dmpc.itp that comes from Dr. Tielman website, such that the residue name follows the 54A7 convention? Renaming the residue is not the problem; you can call a residue whatever you like. The problem is in replacing atom types that are part of the parent force field. The Berger lipids use their own atom types for the lipid atoms; you have to reassign them with 54A7 atom types. Then you have to decide if the charges are still adequate after you've messed with the atom types. The reason I want to use the lipid without Berger lipid is that there's a recent paper http://pubs.acs.org/doi/abs/10.1021/ct300675z that suggests that 54A7 is the better united atom FF as compared to the other FF commonly used, including the Berger Gromos combination. What is your opinion? Reasonable arguments can be made for a variety of lipid parameter sets. You may want to consider http://md.chem.rug.nl/cgmartini/index.php/blog/269-jungle2. -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] bonded interactions in Gromos96
On 10/11/13 12:40 PM, Ehsan Sadeghi wrote: Hi gromacs users, I tried to add new bonded interactions to the ffbonded.itp file in gromos96, but I am confused about the used parameters in the descriptions. Here is an example: #define gb_10.1000 1.5700e+07 ; H - OA 750 The equation used in gromos is Vb(r_ij)=(1/4) k_ij (r_ij^2 - b_ij^2)^2 I see two unknowns: k_ij and b_ij; but there are 3 numbers in the definition: 0.1000, 1.5700e+07, 750. The same story for the angle potential: #define ga_1 90.00 380.00 ; NR(heme) - FE - C 90 The equation used in gromos is Va(theta_ijk)=(1/2) k_ijk (cos(theta_ijk) - cos(theta0_ijk))^2 I see two unknowns: k_ijk and theta0_ijk; but there are 3 numbers in the definition: 90.00, 380, 90. The numbers in the comment lines are bond indices from the Gromos96 force field files. They are irrelevant. -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] bonded interactions in Gromos96
On 10/11/13 1:31 PM, Ehsan Sadeghi wrote: Thanks Justin. Do you know how can I find these coefficients for the atom interactions which are not defined in Gromos? I have (-(CF2CF2)4 -)(-O-CF2CF(CF3 )-O-CF2 CF2-SO3H) molecule. I need C-F, C-S, C-S-O interactions. Can I use predefined ones? which one? Bond lengths typically come from crystallography and force constants from spectroscopy. If they don't already exist in the parent force field and no one has derived them in subsequent work, you're stuck deriving them yourself based on whatever experimental evidence is available. -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
[gmx-users] energy drift - comparison of double and single precision
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. 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 -- 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
Hi, Guillaume- No one can tell you if you did anything wrong if you didn't tell us what you did! There are literally thousands of combinations of options in running an NVE simulation, a substantial fraction of which are guaranteed not to conserve energy. If you post the files (inputs and relevant output files) to redmine.gromacs.org, then people would be able to see if it was an error in how you ran the simulation, or an actual bug. On Fri, Oct 11, 2013 at 1:58 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. 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 -- 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
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
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
Re: [gmx-users] energy drift - comparison of double and single precision
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. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
