Re: [gmx-users] Gromacs GPU got hang
Hi Szilárd,
I tried to use strace to one of the MPI ranks. Below are the outputs. There
are some timed out in OpenMP thread, but I have no idea what is the root
cause. Is it kind of bug in Gromacs, or maybe in MPI / OpenMP ? Could you
see what's the root cause ?
FYI, we use Intel compiler v15.0.2 and OpenMPI v1.8.8. In this simulation,
I use 4 MPI ranks and each rank has 4 OpenMP threads.
PIDs of the MPI processes:
$ ps -axf
3014 ?Sl16:50 /opt/gridengine/bin/linux-x64/sge_execd
3027 ?S 2:37 \_ /opt/gridengine/util/gpu/gpu_sensor
12938 ?S 0:00 \_ sge_shepherd-407 -bg
12967 ?Ss 0:00 \_ -bash
/opt/gridengine/apollo4/spool/apollo4-g01/job_scripts/407
12987 ?Sl 0:00 \_ mpirun -np 4 gmx_mpi mdrun -deffnm
md -pin on -pinoffset 0 -gpu_id
12989 ?Sl 4680:09 \_ gmx_mpi mdrun -deffnm md -pin
on -pinoffset 0 -gpu_id
12990 ?Sl 4681:36 \_ gmx_mpi mdrun -deffnm md -pin
on -pinoffset 0 -gpu_id
12991 ?Sl 4681:17 \_ gmx_mpi mdrun -deffnm md -pin
on -pinoffset 0 -gpu_id
12992 ?Sl 4681:25 \_ gmx_mpi mdrun -deffnm md -pin
on -pinoffset 0 -gpu_id
strace one of MPI processes
[root@apollo4-g01 strace407]# strace -s 128 -x -p 12989 -f 2>&1 | head -50
Process 12989 attached with 9 threads
[pid 13039] restart_syscall(<... resuming interrupted call ...>
[pid 13031] futex(0x2b428203be84, FUTEX_WAIT_PRIVATE, 3, NULL
[pid 13025] futex(0x2b428205d484, FUTEX_WAIT_PRIVATE, 5, NULL
[pid 13024] futex(0x2b428205e984, FUTEX_WAIT_PRIVATE, 5, NULL
[pid 13023] restart_syscall(<... resuming interrupted call ...>
[pid 13020] restart_syscall(<... resuming interrupted call ...>
[pid 13005] select(23, [12 16 22], [], NULL, NULL
[pid 12995] restart_syscall(<... resuming interrupted call ...>
[pid 12989] futex(0x2b428205f784, FUTEX_WAIT_PRIVATE, 1, NULL
[pid 13039] <... restart_syscall resumed> ) = 0
[pid 13039] clock_gettime(CLOCK_MONOTONIC_RAW, {3330079, 937607479}) = 0
[pid 13039] clock_gettime(CLOCK_MONOTONIC_RAW, {3330079, 937666819}) = 0
[pid 13039] poll([{fd=38, events=POLLIN}, {fd=40, events=POLLIN}, {fd=41,
events=POLLIN}, {fd=42, events=POLLIN}, {fd=43, events=POLLIN}, {fd=45,
events=POLLIN}], 6, 100) = 0 (Timeout)
[pid 13039] clock_gettime(CLOCK_MONOTONIC_RAW, {3330080, 38112431}) = 0
[pid 13039] clock_gettime(CLOCK_MONOTONIC_RAW, {3330080, 38178662}) = 0
[pid 13039] poll([{fd=38, events=POLLIN}, {fd=40, events=POLLIN}, {fd=41,
events=POLLIN}, {fd=42, events=POLLIN}, {fd=43, events=POLLIN}, {fd=45,
events=POLLIN}], 6, 100
*[pid 13023] <... restart_syscall resumed> ) = -1 ETIMEDOUT (Connection
timed out)*
[pid 13023] futex(0x2b426ed9aa00, FUTEX_WAKE_PRIVATE, 1) = 0
[pid 13023] futex(0x2b426ed9aa44,
FUTEX_WAIT_BITSET_PRIVATE|FUTEX_CLOCK_REALTIME, 1103881, {1444684996,
236306000},
[pid 13039] <... poll resumed> )= 0 (Timeout)
[pid 13039] clock_gettime(CLOCK_MONOTONIC_RAW, {3330080, 138386651}) = 0
[pid 13039] clock_gettime(CLOCK_MONOTONIC_RAW, {3330080, 138430809}) = 0
[pid 13039] poll([{fd=38, events=POLLIN}, {fd=40, events=POLLIN}, {fd=41,
events=POLLIN}, {fd=42, events=POLLIN}, {fd=43, events=POLLIN}, {fd=45,
events=POLLIN}], 6, 100) = 0 (Timeout)
[pid 13039] clock_gettime(CLOCK_MONOTONIC_RAW, {3330080, 238630125}) = 0
[pid 13039] clock_gettime(CLOCK_MONOTONIC_RAW, {3330080, 238673628}) = 0
[pid 13039] poll([{fd=38, events=POLLIN}, {fd=40, events=POLLIN}, {fd=41,
events=POLLIN}, {fd=42, events=POLLIN}, {fd=43, events=POLLIN}, {fd=45,
events=POLLIN}], 6, 100
[pid 13023] <... futex resumed> ) = -1 ETIMEDOUT (Connection timed
out)
[pid 13023] futex(0x2b426ed9aa00, FUTEX_WAKE_PRIVATE, 1) = 0
[pid 13023] futex(0x2b426ed9aa44,
FUTEX_WAIT_BITSET_PRIVATE|FUTEX_CLOCK_REALTIME, 1103883, {1444684996,
436466000},
[pid 13039] <... poll resumed> )= 0 (Timeout)
[pid 13039] clock_gettime(CLOCK_MONOTONIC_RAW, {3330080, 338874153}) = 0
[pid 13039] clock_gettime(CLOCK_MONOTONIC_RAW, {3330080, 338918688}) = 0
*[pid 13039] poll([{fd=38, events=POLLIN}, {fd=40, events=POLLIN}, {fd=41,
events=POLLIN}, {fd=42, events=POLLIN}, {fd=43, events=POLLIN}, {fd=45,
events=POLLIN}], 6, 100) = 0 (Timeout)*
[pid 13039] clock_gettime(CLOCK_MONOTONIC_RAW, {3330080, 439131341}) = 0
[pid 13039] clock_gettime(CLOCK_MONOTONIC_RAW, {3330080, 439174001}) = 0
[pid 13039] poll([{fd=38, events=POLLIN}, {fd=40, events=POLLIN}, {fd=41,
events=POLLIN}, {fd=42, events=POLLIN}, {fd=43, events=POLLIN}, {fd=45,
events=POLLIN}], 6, 100
*[pid 13023] <... futex resumed> ) = -1 ETIMEDOUT (Connection timed
out)*
[pid 13023] futex(0x2b426ed9aa00, FUTEX_WAKE_PRIVATE, 1) = 0
[pid 13023] futex(0x2b426ed9aa44,
FUTEX_WAIT_BITSET_PRIVATE|FUTEX_CLOCK_REALTIME, 1103885, {1444684996,
636581000},
[pid 13039] <... poll resumed> )= 0 (Timeout)
[pid 13039] clock_gettime(CLOCK_MONOTONIC_RAW, {3330080, 539370079}) = 0
[pid 13039] clock_gettim
Re: [gmx-users] velocity in trjconv
Hi, Probably you should use '-novel' On Mon, Oct 12, 2015 at 10:23 PM, Parvez Mh wrote: > Dear all, > I need to convert .trr file into .gro file without velocity. That's why i > used '-vel no' , but i got error 'invalid argument no'. Can any tell me how > to use -vel option for not writing velocity in .gro file . > > Regards > Masrul > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] output control
Yes of course! That would be so kind of you to send the editor and a brief description of how it works. Thanks a lot tsjerk. On Monday, October 12, 2015, Tsjerk Wassenaar wrote: > Hi Maryam, > > You only need a modified TPR file. There's no need to hassle with > structures, as that's all in the checkpoint file. > > I have a TPR editor that allows changing things like nstxout. So you can > run the first part of the simulation, then modify the TPR nstxout and > nsteps, and continue the simulation from the last checkpoint file. If you > want, I can send that. > > Cheers, > > Tsjerk > On Oct 12, 2015 5:35 PM, "Maryam Kowsar" > wrote: > > > Thanks Mark and Pierre. > > > > I would rather try Mark's solution but I exactly dont understand what I > > should do now! I used 2 sets of commands > > > > tpbconv -s previous.tpr -extend timetoextendby -o next.tpr > > > > mdrun -s next.tpr -cpi previous.cpt > > > > OR > > > > tpbcov -s -o new.tpr -extend 20 > > > > grompp -f new.mdp(NSTXOUT=1) -c old.tpr -o new.tpr > > > > mdrun -s new.tpr -cpi > > > > which will generate 200G data! > > > > your help is needed! > > > > Thanks. > > > > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org . > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org . -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] velocity in trjconv
On 10/12/15 12:53 PM, Parvez Mh wrote: Dear all, I need to convert .trr file into .gro file without velocity. That's why i used '-vel no' , but i got error 'invalid argument no'. Can any tell me how to use -vel option for not writing velocity in .gro file . As with all GROMACS boolean options, the formation is -option/-nooption, so in this case specifically the proper syntax is -novel. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] velocity in trjconv
Dear all, I need to convert .trr file into .gro file without velocity. That's why i used '-vel no' , but i got error 'invalid argument no'. Can any tell me how to use -vel option for not writing velocity in .gro file . Regards Masrul -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] output control
Hi Maryam, You only need a modified TPR file. There's no need to hassle with structures, as that's all in the checkpoint file. I have a TPR editor that allows changing things like nstxout. So you can run the first part of the simulation, then modify the TPR nstxout and nsteps, and continue the simulation from the last checkpoint file. If you want, I can send that. Cheers, Tsjerk On Oct 12, 2015 5:35 PM, "Maryam Kowsar" wrote: > Thanks Mark and Pierre. > > I would rather try Mark's solution but I exactly dont understand what I > should do now! I used 2 sets of commands > > tpbconv -s previous.tpr -extend timetoextendby -o next.tpr > > mdrun -s next.tpr -cpi previous.cpt > > OR > > tpbcov -s -o new.tpr -extend 20 > > grompp -f new.mdp(NSTXOUT=1) -c old.tpr -o new.tpr > > mdrun -s new.tpr -cpi > > which will generate 200G data! > > your help is needed! > > Thanks. > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] output control
Thanks Mark and Pierre. I would rather try Mark's solution but I exactly dont understand what I should do now! I used 2 sets of commands tpbconv -s previous.tpr -extend timetoextendby -o next.tpr mdrun -s next.tpr -cpi previous.cpt OR tpbcov -s -o new.tpr -extend 20 grompp -f new.mdp(NSTXOUT=1) -c old.tpr -o new.tpr mdrun -s new.tpr -cpi which will generate 200G data! your help is needed! Thanks. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Is diffusion coefficient dependent on box size?
How long are your simulations? Have you looked at your msd.xvg files to make sure you have a "straight" line in the fitting region? -Micholas === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Pallavi Banerjee Sent: Monday, October 12, 2015 10:49 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Is diffusion coefficient dependent on box size? Hello Users, On simulating SPC-E water, I see that I get two different values of diffusion coefficient from two different box sizes. I get D=2.4 from a cubic box of 3 nm and D=2.7 from a cubic box of 7 nm. All the .mdp parameters are the same for both. The diffusion coefficients are obtained from g_msd Any idea what could be going wrong here? Thanks in advance! -Pallavi Banerjee -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Is diffusion coefficient dependent on box size?
On 10/12/15 10:49 AM, Pallavi Banerjee wrote: Hello Users, On simulating SPC-E water, I see that I get two different values of diffusion coefficient from two different box sizes. I get D=2.4 from a cubic box of 3 nm and D=2.7 from a cubic box of 7 nm. All the .mdp parameters are the same for both. The diffusion coefficients are obtained from g_msd Any idea what could be going wrong here? There are finite size effects in computing diffusion coefficients. See dx.doi.org/10.1021/jp0477147 -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Construction of silver nanoparticles
On 10/12/15 7:20 AM, SAPNA BORAH wrote: Dear All, I am trying to perform silver nanoparticles simulations. Since I found articles performing such simulations in gromacs, I have a query against how do I incorporate the silver atoms in the simulation box? Perhaps contact the corresponding author(s) of the study(ies) you find most relevant to your work? -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Is diffusion coefficient dependent on box size?
Hello Users, On simulating SPC-E water, I see that I get two different values of diffusion coefficient from two different box sizes. I get D=2.4 from a cubic box of 3 nm and D=2.7 from a cubic box of 7 nm. All the .mdp parameters are the same for both. The diffusion coefficients are obtained from g_msd Any idea what could be going wrong here? Thanks in advance! -Pallavi Banerjee -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Message-ID: Content-Type: text/plain; charset=UTF-8
Hi, On Mon, Oct 12, 2015 at 3:31 PM Kim Jessica Novacek < kim.j.nova...@campus.lmu.de> wrote: > Although I did let out the Xeon Phi Command there is still the same make > error. > Greetings > Kim > > > /usr/bin/ld: cannot find -lcudart > /usr/bin/ld: cannot find -lmpi > collect2: error: ld returned 1 exit status > make[2]: *** [bin/gmx_mpi] Fehler 1 > make[1]: *** [src/programs/CMakeFiles/gmx.dir/all] Fehler 2 > make[1]: *** Auf noch nicht beendete Prozesse wird gewartet … > /usr/bin/ld: cannot find -lcudart > /usr/bin/ld: cannot find -lmpi > collect2: error: ld returned 1 exit status > make[2]: *** [bin/template] Fehler 1 > make[1]: *** [share/template/CMakeFiles/template.dir/all] Fehler 2 > make: *** [all] Fehler 2 > > > cmake .. -DREGRESSIONTEST_DOWNLOAD=ON -DCMAKE_C_COMPILER=/usr/bin/gcc > -DGMX_MPI=ON -DGMX_GPU=ON > -DCUDA_TOOLKIT_ROOT_DIR=/usr/lib/nvidia-cuda-toolkit > -DCMAKE_INSTALL_PREFIX=/usr/local/GROMACS -DGMX_FFT_LIBRARY=fftw3 > -DFFTWF_LIBRARY=/usr/local/lib/libfftw3f.a -DCMAKE_BUILD_TYPE=DEBUG > -DCMAKE_CXX_COMPILER=/usr/bin/gcc -DGMX_PREFER_STATIC_LIBS=ON > -DCMAKE_C_FLAGS="-static" -DCMAKE_CXX_FLAGS="-static" > -DCMAKE_SKIP_RPATH=YES -DCMAKE_PREFIX_PATH=/usr/lib/cuda > -DCMAKE_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu/libcudart.so > -DCMAKE_PREFIX_PATH=/usr/include/libxml2/libxml > Setting CMAKE_LIBRARY_PATH to an actual file, which is then the one that can't be found seems like a bad thing to do. That path is a standard system path, so if you want to find that library, you can probably leave it alone. But you will get this library via the CUDA toolkit you already asked for, if the toolkit is installed correctly and you're using it the way the sysadmins intended you to use it. Your system should have an MPI wrapper compiler - find out what it is and use it. Maybe there's even a documented way to compile for MPI+CUDA :-) Mark > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Message-ID: Content-Type: text/plain; charset=UTF-8
Although I did let out the Xeon Phi Command there is still the same make error. Greetings Kim /usr/bin/ld: cannot find -lcudart /usr/bin/ld: cannot find -lmpi collect2: error: ld returned 1 exit status make[2]: *** [bin/gmx_mpi] Fehler 1 make[1]: *** [src/programs/CMakeFiles/gmx.dir/all] Fehler 2 make[1]: *** Auf noch nicht beendete Prozesse wird gewartet … /usr/bin/ld: cannot find -lcudart /usr/bin/ld: cannot find -lmpi collect2: error: ld returned 1 exit status make[2]: *** [bin/template] Fehler 1 make[1]: *** [share/template/CMakeFiles/template.dir/all] Fehler 2 make: *** [all] Fehler 2 cmake .. -DREGRESSIONTEST_DOWNLOAD=ON -DCMAKE_C_COMPILER=/usr/bin/gcc -DGMX_MPI=ON -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/lib/nvidia-cuda-toolkit -DCMAKE_INSTALL_PREFIX=/usr/local/GROMACS -DGMX_FFT_LIBRARY=fftw3 -DFFTWF_LIBRARY=/usr/local/lib/libfftw3f.a -DCMAKE_BUILD_TYPE=DEBUG -DCMAKE_CXX_COMPILER=/usr/bin/gcc -DGMX_PREFER_STATIC_LIBS=ON -DCMAKE_C_FLAGS="-static" -DCMAKE_CXX_FLAGS="-static" -DCMAKE_SKIP_RPATH=YES -DCMAKE_PREFIX_PATH=/usr/lib/cuda -DCMAKE_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu/libcudart.so -DCMAKE_PREFIX_PATH=/usr/include/libxml2/libxml -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] bond lenght distribution?
Hi, You'll need to be more specific. What exact call to g_bond are you saying can't be replicated in later versions? What have you tried? Mark On Mon, Oct 12, 2015 at 3:16 PM Frank Zack wrote: > Hi justin, > thx for your reply. I already read the page referenced in your link. I > know that gmx bond is replaced by gmx distance. But its not the same. I > need the particle distances of bonded particles only... > > > > Justin Lemkul schrieb am 2:43 Montag, 12.Oktober > 2015: > > > > > On 10/11/15 7:23 PM, Frank Zack wrote: > > Hi, > > how can I compute the bond-lenght distribution of my trajectory? I used > to use gmx bond, but now im using VERSION 5.0.7-dev-20151003-1909f2f-dirty > and there is no such tool. I can only calculate inter-particle distances. > But this is not the same as bondlengths. > > http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0#g_bond > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] bond lenght distribution?
Hi justin, thx for your reply. I already read the page referenced in your link. I know that gmx bond is replaced by gmx distance. But its not the same. I need the particle distances of bonded particles only... Justin Lemkul schrieb am 2:43 Montag, 12.Oktober 2015: On 10/11/15 7:23 PM, Frank Zack wrote: > Hi, > how can I compute the bond-lenght distribution of my trajectory? I used to > use gmx bond, but now im using VERSION 5.0.7-dev-20151003-1909f2f-dirty and > there is no such tool. I can only calculate inter-particle distances. But > this is not the same as bondlengths. http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0#g_bond -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Solvent density around a Protein
Hello, I want to examine a Myoglobine-ethylene glycole-water system and I am trying to calculate the density of ethylene glycole and the density of water around residues of Myoglobin (for example Valine). In the mailinglist I found the advice to use the gromacs tool g_sorient to get a distribution of the solvent molecules as a function of the radius around a reference point. One can find in the manual that the solvent molecules should consist of 3 atoms. So I can easily do this for water (3 atoms). I tried using g_sorient for ethylene glycole (6 atoms) too but the ethylene glycole distribution seems to be twice as high as they should be. Now I am asking myself whether the real ethylene glycole distribution is exactly the half of the values that gromacs calculates? In case I get completely wrong values for the distribution, is there another tool to calculate the ethylene glycole distribution around protein residues? Thanks in advance, Maik -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Construction of silver nanoparticles
Dear All, I am trying to perform silver nanoparticles simulations. Since I found articles performing such simulations in gromacs, I have a query against how do I incorporate the silver atoms in the simulation box? Thanks in Advance. Sapna Mayuri Borah c/o Dr. A. N. Jha Research student Tezpur University, India -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] output control
Hi, Please see the link I provided. Pierre's technique is exactly how to make a discontinuous simulation. Whether that matters is a different question, but the checkpoint file can be passed to grompp to make an exact continuation, so do that. Mark On Mon, 12 Oct 2015 10:01 Pierre Ghesquiere wrote: > Hi, > > I dont see any reason why you could not stop the trajectories : indeed > you can always take the last structure (the .gro file) as an input for > the next one. Then, you can use the output of the second simulation > being the input of your third if I get what you mean. > > -- > P. > > Maryam Kowsar a écrit : > > > Thanks Pierre. > > What if I dont want to stop the simulation and use its output as the > input > > for the next simulation? > > > > On Mon, Oct 12, 2015 at 10:15 AM, Pierre Ghesquiere < > > pierre.ghesqui...@univ-perp.fr> wrote: > > > >> Hi, > >> > >> I think you could do two successive trajectories. One during the 1.8 ns > >> and another of 200ps. Then you use different writing frequencies for the > >> two simulations. > >> > >> -- > >> P. > >> > >> Maryam Kowsar a écrit : > >> > >> Dear users, > >>> > >>> I have a simulation which lasts in 2ns and has around 4G trajectory if > >>> Iset > >>> nstxout = 1000. I need the output file of coordinates and velocities > >>> written every step which means a 4000G output file! Is there a way > that I > >>> can manage the tarjectory so that only in the last 200ps of simulation > it > >>> is written every step? If not, can I set nstxout = 1000 and get data > for > >>> every step after the simulation? > >>> > >>> Thank you. > >>> -- > >>> Gromacs Users mailing list > >>> > >>> * Please search the archive at > >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >>> posting! > >>> > >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>> > >>> * For (un)subscribe requests visit > >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >>> send a mail to gmx-users-requ...@gromacs.org. > >>> > >>> > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-requ...@gromacs.org. > >> > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > > or send a mail to gmx-users-requ...@gromacs.org. > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] output control
Hi, I dont see any reason why you could not stop the trajectories : indeed you can always take the last structure (the .gro file) as an input for the next one. Then, you can use the output of the second simulation being the input of your third if I get what you mean. -- P. Maryam Kowsar a écrit : Thanks Pierre. What if I dont want to stop the simulation and use its output as the input for the next simulation? On Mon, Oct 12, 2015 at 10:15 AM, Pierre Ghesquiere < pierre.ghesqui...@univ-perp.fr> wrote: Hi, I think you could do two successive trajectories. One during the 1.8 ns and another of 200ps. Then you use different writing frequencies for the two simulations. -- P. Maryam Kowsar a écrit : Dear users, I have a simulation which lasts in 2ns and has around 4G trajectory if Iset nstxout = 1000. I need the output file of coordinates and velocities written every step which means a 4000G output file! Is there a way that I can manage the tarjectory so that only in the last 200ps of simulation it is written every step? If not, can I set nstxout = 1000 and get data for every step after the simulation? Thank you. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] output control
Hi, That's one reason why we write checkpoints that permit exact restarts. See http://www.gromacs.org/Documentation/How-tos/Extending_Simulations Mark On Mon, Oct 12, 2015 at 8:55 AM Maryam Kowsar wrote: > Thanks Pierre. > What if I dont want to stop the simulation and use its output as the input > for the next simulation? > > On Mon, Oct 12, 2015 at 10:15 AM, Pierre Ghesquiere < > pierre.ghesqui...@univ-perp.fr> wrote: > > > Hi, > > > > I think you could do two successive trajectories. One during the 1.8 ns > > and another of 200ps. Then you use different writing frequencies for the > > two simulations. > > > > -- > > P. > > > > Maryam Kowsar a écrit : > > > > Dear users, > >> > >> I have a simulation which lasts in 2ns and has around 4G trajectory if > >> Iset > >> nstxout = 1000. I need the output file of coordinates and velocities > >> written every step which means a 4000G output file! Is there a way that > I > >> can manage the tarjectory so that only in the last 200ps of simulation > it > >> is written every step? If not, can I set nstxout = 1000 and get data for > >> every step after the simulation? > >> > >> Thank you. > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-requ...@gromacs.org. > >> > >> > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
