[gmx-users] Several questions about the GPU version
Hey guys, Meanwhile I run my simulations on a CUDA card and must say that I am very very satisfied with it. Nevertheless I have a few questions regarding to a improved performance: 1. Is it possible to perform the PME calculation on the CUDA card? I always see in md.log that the PME runs on the CPU, even if the flag -nb gpu is set. 2. Is it possible to run multiple simulations on one CUDA card? If so, how and is there an engine program for the management (like on clusters)? 3. I don't understand the sense of the mdp option coulomb-modifier. What should it cause? I set it to none. It would be very nice if someone or some people could answer the questions. Many thanks and best, grita -- View this message in context: http://gromacs.5086.x6.nabble.com/Several-questions-about-the-GPU-version-tp5010934.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] (no subject)
Respected sir, I am facing a problem while simulating the tRNA molecule while converting pdb to gro, Fatal error: Atom OP3 in residue A 1 was not found in rtp entry RA5 with 31 atoms while sorting atoms. force field used 3 (AMBER96 protein, nucleic AMBER94), water model TIP3P. kindly give valuable suggestion how to rectify this error, Awaiting For your reply Thanking You -- 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] (no subject)
On 9/3/13 7:20 AM, Prajisha Sujaya wrote: Respected sir, I am facing a problem while simulating the tRNA molecule while converting pdb to gro, Fatal error: Atom OP3 in residue A 1 was not found in rtp entry RA5 with 31 atoms while sorting atoms. force field used 3 (AMBER96 protein, nucleic AMBER94), water model TIP3P. kindly give valuable suggestion how to rectify this error, http://www.gromacs.org/Documentation/Errors#Atom_X_in_residue_YYY_not_found_in_rtp_entry -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] Position Restrained of ions
Dear Gmx Users, i wish I could restrain some ions in my system (NA). I tried to include it in ions.itp: [ moleculetype ] ; molnamenrexcl NA1 #ifdef POSRES_NA [ position_restraints ] ; atom type fx fy fz 1 1 1000 1000 1000 #endif But it does not work. Would you advise please? Steven -- 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] Select atoms in a residue
Hello all, A Quick question below: My peptide contains one trp, and i want to select only the atoms that form the the indol ring. I would like a portable script for others systems that contain also a peptide with one Trp residue. So I am not interesting to select the corresponding atoms by their numbers in the pdb/gro files The atom name in the indol group are aCG | aCD1 | aHD1 | aCD2 | aCE3 | aHE3 | aCZ3 | aHZ3 | aCH2 | aHH2 | aCZ2 | aHZ2 | aCE2 | aNE1 | aHE1 Can you help me ? Best, Stephane -- 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] Position Restrained of ions
On 9/3/13 8:14 AM, Steven Neumann wrote: Dear Gmx Users, i wish I could restrain some ions in my system (NA). I tried to include it in ions.itp: [ moleculetype ] ; molnamenrexcl NA1 #ifdef POSRES_NA [ position_restraints ] ; atom type fx fy fz 1 1 1000 1000 1000 #endif But it does not work. Would you advise please? Please define what does not work means. -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] Select atoms in a residue
On 9/3/13 8:57 AM, ABEL Stephane 175950 wrote: Hello all, A Quick question below: My peptide contains one trp, and i want to select only the atoms that form the the indol ring. I would like a portable script for others systems that contain also a peptide with one Trp residue. So I am not interesting to select the corresponding atoms by their numbers in the pdb/gro files The atom name in the indol group are aCG | aCD1 | aHD1 | aCD2 | aCE3 | aHE3 | aCZ3 | aHZ3 | aCH2 | aHH2 | aCZ2 | aHZ2 | aCE2 | aNE1 | aHE1 Can you help me ? What is the problem? Aside from a lack of a space between the 'a' and the actual atom name, that should work just fine. -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] Steered MD in gromacs
Dear all, I am just starting MD simulations and wanted to see how to perform steered molecular dynamics in gromacs . Most papers and tutorials that I found were done in NAMD. Can anyone recommend examples that were done in gromacs? In my case the tutorial Pull Code and Umbrella Sampling on the gromacs website seems not applicable. I simply want to see how to perform an in vacuo simulation by pulling. Thank you in advance!! -- 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] Re: Select atoms in a residue
On 9/3/13 11:36 AM, ABEL Stephane 175950 wrote: Hello Justin, My question was How to select the following atoms CG, CD1, HD1, CD2, CE3, HE3, CZ3, HZ3, CH2, etc.. present ONLY in the trp residue with a single line command with make_ndx. Indeed some of them can be also present in other residues. r TRP a CG | a CD1 | ... -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] Several questions about the GPU version
On Tue, Sep 3, 2013 at 9:37 AM, grita cemilyi...@arcor.de wrote: Hey guys, Meanwhile I run my simulations on a CUDA card and must say that I am very very satisfied with it. Nevertheless I have a few questions regarding to a improved performance: 1. Is it possible to perform the PME calculation on the CUDA card? I always see in md.log that the PME runs on the CPU, even if the flag -nb gpu is set. I answered this last week. Was there something unsatisfactory about that answer? :-) 2. Is it possible to run multiple simulations on one CUDA card? If so, how and is there an engine program for the management (like on clusters)? Yes, but there is nothing fancy for it. See http://www.gromacs.org/Documentation/Acceleration_and_parallelization. You should just run multiple instances of mdrun, being sure to specify a suitable number of threads so that your total usage fills all your CPU cores. You will need to use the mdrun pinning options to pin threads to cores manually, since mdrun will detect that it does not have the CPU to itself, so it will not make unwarranted assumptions about whether pinning is acceptable. 3. I don't understand the sense of the mdp option coulomb-modifier. What should it cause? I set it to none. Have you checked out the appropriate part of manual 7.3? Mark It would be very nice if someone or some people could answer the questions. Many thanks and best, grita -- View this message in context: http://gromacs.5086.x6.nabble.com/Several-questions-about-the-GPU-version-tp5010934.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 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] Steered MD in gromacs
On 9/3/13 11:22 AM, hanna pdb wrote: Dear all, I am just starting MD simulations and wanted to see how to perform steered molecular dynamics in gromacs . Most papers and tutorials that I found were done in NAMD. Can anyone recommend examples that were done in gromacs? In my case the tutorial Pull Code and Umbrella Sampling on the gromacs website seems not applicable. I simply want to see how to perform an in vacuo simulation by pulling. Indeed, my tutorial will go beyond what you want, but I don't see how it's not applicable. There is discussion of how to use all (or at least most) of the pull settings and produce a SMD trajectory as part of the protocol. -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] Re: Select atoms in a residue
Hello Justin, My question was How to select the following atoms CG, CD1, HD1, CD2, CE3, HE3, CZ3, HZ3, CH2, etc.. present ONLY in the trp residue with a single line command with make_ndx. Indeed some of them can be also present in other residues. Stephane -- Message: 4 Date: Tue, 3 Sep 2013 12:57:25 + From: ABEL Stephane 175950 stephane.a...@cea.fr Subject: [gmx-users] Select atoms in a residue To: gmx-users@gromacs.org gmx-users@gromacs.org Message-ID: 3e39b768bb199548ab18f7289e7534af1a880...@exdag0-b0.intra.cea.fr Content-Type: text/plain; charset=us-ascii Hello all, A Quick question below: My peptide contains one trp, and i want to select only the atoms that form the the indol ring. I would like a portable script for others systems that contain also a peptide with one Trp residue. So I am not interesting to select the corresponding atoms by their numbers in the pdb/gro files The atom name in the indol group are aCG | aCD1 | aHD1 | aCD2 | aCE3 | aHE3 | aCZ3 | aHZ3 | aCH2 | aHH2 | aCZ2 | aHZ2 | aCE2 | aNE1 | aHE1 Can you help me ? Best, Stephane -- 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] AVX libraries with GMX4.6.3
Hi Mark, 1e-9 is indeed an abnormally high tolerance to use, I was just testing higher precisions to see if I can get better energy conservation. I ran some 1ns tests with different tolerances and compared avx and sse instruction sets. I'm still seeing a discrepancy between the two instruction sets as can be seen; AVX : https://www.dropbox.com/s/glmhyj1l18va8xp/avx_tol_comp_2.png SSE : https://www.dropbox.com/s/6bwz4j9d0xywe2w/sse_tol_comp_2.png where in SET_TEMP_X, SET=the instruction set used for the binary compilation and X=(ewald_rtol=1e-X). For X=5,6,7 they are basically the same but for X=8,9 SSE is an order of magnitude better than AVX. For a more normal value like X=5,6 the acceleration types certainly agree so this might not be very important but I wanted to post what I have seen nonetheless. Best, Ali Sinan Saglam On Fri, Aug 30, 2013 at 2:32 PM, Mark Abraham mark.j.abra...@gmail.comwrote: ewald_rtol of 1e-9 is a very long way from the normal range of values, and your other electrostatics settings seem pretty normal. I'd expect these results to be of doubtful value, but I am surprised to see that/if there is a marked different with acceleration type. I suggest you try a normal simulation protocol and see how you go. Mark On Fri, Aug 30, 2013 at 7:31 PM, Ali Sinan Saglam asinansag...@gmail.com wrote: Hi Mark, I have tried GCC 4.7.1, 4.7.2 and ICC 13 (with and without MKL, my colleague also tried double precision) compilers, all showed the same behavior. I will add the .mdp file I have used but the problem consists for all input files my colleagues tried (they had their own input files, independent to me). For example the first graph is Barnase - Barstar in a large box (~100,000 atoms, explicit tip3p waters, neutralized and a small amount of salt, roughly 60-70 atoms of NaCl) and the mdp file used was; ;# INTEGRATOR ## integrator = md; Molecular dynamics dt = 0.002 ; Timestep (ps) nsteps = 50; Simulation duration (timesteps) nstcomm = 1000 ; Center of mass motion removal interval (timesteps) comm-grps = system; Remove center of mass motion of system ;## ENSEMBLE ### Pcoupl = no; Disable barostat tcoupl = no; Disable thermostat ; BONDED INTERACTIONS ## constraints = hbonds; Disable constraints constraint_algorithm= LINCS ; Constrain bonds using LINCS lincs_iter = 1 ; Number of LINCS iterations ;### NONBONDED INTERACTIONS coulombtype = PME ; Switch/PME long-range electrostatics fourierspacing = 0.1 pme_order = 4 ewald_rtol = 0.1 pbc = xyz ; Periodic boundary condition rcoulomb= 1.00 ; Short-range electrostatic cutoff (nm) ;rcoulomb_switch = 0.9 ; Short-range electrostatic switch cutoff (nm) vdwtype = Switch; Switch van der Waals interactions rvdw= 0.9 ; Van der Waals cutoff (nm) rvdw_switch = 0.8 ; Van der Waals switch cutoff (nm) DispCorr= EnerPres ; Long-range dispersion correction to energy and pressure ns_type = grid ; Update neighbor list using grid nstlist = 10; Neighbor list update interval (timesteps) rlist = 1.00 ; Neighbor list cut-off (nm) continuation= yes ;### OUTPUT nstlog = 500 ; Energy log output interval (timesteps) nstenergy = 50; Energy output interval (timesteps) nstxout = 50; Full-resolution trajectory
Re: [gmx-users] AVX libraries with GMX4.6.3
On Tue, Sep 3, 2013 at 6:17 PM, Ali Sinan Saglam asinansag...@gmail.com wrote: Hi Mark, 1e-9 is indeed an abnormally high tolerance to use, I was just testing higher precisions to see if I can get better energy conservation. Did you read all of what manual section 7.3 has to say about the ewald_rtol parameter? I ran some 1ns tests with different tolerances and compared avx and sse instruction sets. I'm still seeing a discrepancy between the two instruction sets as can be seen; AVX : https://www.dropbox.com/s/glmhyj1l18va8xp/avx_tol_comp_2.png SSE : https://www.dropbox.com/s/6bwz4j9d0xywe2w/sse_tol_comp_2.png where in SET_TEMP_X, SET=the instruction set used for the binary compilation and X=(ewald_rtol=1e-X). For X=5,6,7 they are basically the same but for X=8,9 SSE is an order of magnitude better than AVX. For a more normal value like X=5,6 the acceleration types certainly agree so this might not be very important but I wanted to post what I have seen nonetheless. Thanks, but as you will see in your .log files, you are choosing values for ewald_rtol that choose an Ewald splitting parameter beta that probably computes nonsense in the FFTs in concert with the FFT grid in your .mdp - overflow, underflow, accumulation error, whatever. The acceleration setting affects how GROMACS uses SIMD to prepare and/or post-process the FFT, but for all I know the FFT was already nonsense. Mark Best, Ali Sinan Saglam On Fri, Aug 30, 2013 at 2:32 PM, Mark Abraham mark.j.abra...@gmail.comwrote: ewald_rtol of 1e-9 is a very long way from the normal range of values, and your other electrostatics settings seem pretty normal. I'd expect these results to be of doubtful value, but I am surprised to see that/if there is a marked different with acceleration type. I suggest you try a normal simulation protocol and see how you go. Mark On Fri, Aug 30, 2013 at 7:31 PM, Ali Sinan Saglam asinansag...@gmail.com wrote: Hi Mark, I have tried GCC 4.7.1, 4.7.2 and ICC 13 (with and without MKL, my colleague also tried double precision) compilers, all showed the same behavior. I will add the .mdp file I have used but the problem consists for all input files my colleagues tried (they had their own input files, independent to me). For example the first graph is Barnase - Barstar in a large box (~100,000 atoms, explicit tip3p waters, neutralized and a small amount of salt, roughly 60-70 atoms of NaCl) and the mdp file used was; ;# INTEGRATOR ## integrator = md; Molecular dynamics dt = 0.002 ; Timestep (ps) nsteps = 50; Simulation duration (timesteps) nstcomm = 1000 ; Center of mass motion removal interval (timesteps) comm-grps = system; Remove center of mass motion of system ;## ENSEMBLE ### Pcoupl = no; Disable barostat tcoupl = no; Disable thermostat ; BONDED INTERACTIONS ## constraints = hbonds; Disable constraints constraint_algorithm= LINCS ; Constrain bonds using LINCS lincs_iter = 1 ; Number of LINCS iterations ;### NONBONDED INTERACTIONS coulombtype = PME ; Switch/PME long-range electrostatics fourierspacing = 0.1 pme_order = 4 ewald_rtol = 0.1 pbc = xyz ; Periodic boundary condition rcoulomb= 1.00 ; Short-range electrostatic cutoff (nm) ;rcoulomb_switch = 0.9 ; Short-range electrostatic switch cutoff (nm) vdwtype = Switch; Switch van der Waals interactions rvdw= 0.9 ; Van der Waals cutoff (nm) rvdw_switch = 0.8 ; Van der Waals switch cutoff (nm) DispCorr= EnerPres ; Long-range dispersion correction to energy and pressure ns_type = grid ; Update neighbor list using grid nstlist = 10
[gmx-users] gromacs 4.6.3 and Intel compiiler 11.x
Dear GMX users, I'm attempting to compile gromacs 4.6.3 with an older Intel compiler (ver 11.x). Here is how I compiled FFTW, ./configure CC=icc F77=ifort CFLAGS=-O3 -gcc --prefix=/tmp/gromacs-4.6.3/fftw-3.3.3/build-intel-threads --enable-threads --enable-sse2 --with-combined-threads --with-our-malloc16 --enable-float And, here is how I invoked cmake, CC=icc CXX=icpc ../cmake-2.8.11/bin/cmake .. -DGMX_FFT_LIBRARY=fftw3 -DFFTWF_LIBRARY=/tmp/gromacs-4.6.3/fftw-3.3.3/build-intel-threads/lib/libfftw3f.a -DFFTWF_INCLUDE_DIR=/tmp/gromacs-4.6.3/fftw-3.3.3/build-intel-threads/include -DBUILD_SHARED_LIBS=no -DCMAKE_INSTALL_PREFIX=/home/gc603449/APPLICATIONS/gromac-4.6.3/thread-float-static -DREGRESSIONTEST_PATH=/tmp/gromacs-4.6.3/regressiontests-4.6.1 When I ran 'make check', 39 out of 142 kernel tests failed, and 2 out of 9 free energy tests failed. This is my first time to compile gromacs, which I am not very familiar with. I wonder if anyone can kindly point out what has gone wrong, and where to look for hints. Any help is much appreciated. Best regards, -- Guanglei Cui PS: I am aware of a warning about using older Intel compilers with 4.6.3, but that's the only quality compiler I got. The gcc compiler I have access to is too old (ver 4.1.x) -- 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] Error bar for free energy
Hi Dear Gromacs users, I would like to calculate the standard deviation (as the error bar) for dV/dlambda.xvg file. I used g_analyze command as the following: g_analyze -ffree0.9.xvg -av average_0.9 I got: set average*standard deviation**std. dev. / sqrt(n-1)*… SS1 6.053822e+01 3.062230e+01 1.936724e-02 … Is the amount of in third (standard deviation) or fourth column (std. dev. / sqrt(n-1) ) better than to use as the error bar? I want to draw dG/d lambda via lambda and show error bar for free energy differences. Thanks in advance Afsaneh -- 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] psf2top: a tool for converting NAMD PSF files to GROMACS topologies
Hi all, I've written a tool, called psf2top.py which can convert NAMD PSF files directly to GROMACS topologies. It is part of PyTopol package and is available here https://github.com/resal81/PyTopol . Please note that PyTopol is currently in alpha stage. If you test psf2top.py on your PSF files, please let me know about the results here https://github.com/resal81/PyTopol/issues. Thanks, Reza Salari === Reza Salari, Ph.D. Postdoctoral Researcher Brannigan Lab Center for Computational and Integrative Biology Rutgers University-Camden Camden, NJ -- 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 4.6.3 and Intel compiiler 11.x
On 9/3/13 1:47 PM, Guanglei Cui wrote: Dear GMX users, I'm attempting to compile gromacs 4.6.3 with an older Intel compiler (ver 11.x). Here is how I compiled FFTW, ./configure CC=icc F77=ifort CFLAGS=-O3 -gcc --prefix=/tmp/gromacs-4.6.3/fftw-3.3.3/build-intel-threads --enable-threads --enable-sse2 --with-combined-threads --with-our-malloc16 --enable-float And, here is how I invoked cmake, CC=icc CXX=icpc ../cmake-2.8.11/bin/cmake .. -DGMX_FFT_LIBRARY=fftw3 -DFFTWF_LIBRARY=/tmp/gromacs-4.6.3/fftw-3.3.3/build-intel-threads/lib/libfftw3f.a -DFFTWF_INCLUDE_DIR=/tmp/gromacs-4.6.3/fftw-3.3.3/build-intel-threads/include -DBUILD_SHARED_LIBS=no -DCMAKE_INSTALL_PREFIX=/home/gc603449/APPLICATIONS/gromac-4.6.3/thread-float-static -DREGRESSIONTEST_PATH=/tmp/gromacs-4.6.3/regressiontests-4.6.1 When I ran 'make check', 39 out of 142 kernel tests failed, and 2 out of 9 free energy tests failed. This is my first time to compile gromacs, which I am not very familiar with. I wonder if anyone can kindly point out what has gone wrong, and where to look for hints. Any help is much appreciated. Best regards, -- Guanglei Cui PS: I am aware of a warning about using older Intel compilers with 4.6.3, but that's the only quality compiler I got. The gcc compiler I have access to is too old (ver 4.1.x) I assume what you're referring to is http://redmine.gromacs.org/issues/1126, so it should be pretty clear (and cmake reminds you) that there are expected regression test failures with this compiler and SSE4.1. I suppose a workaround is to use a different CPU acceleration, but you'll pay a price in performance. Outdated compilers can't be expected to handle all the best features Gromacs has to offer :) -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 4.6.3 and Intel compiiler 11.x
Hi Justin, Thanks for the response. Right now, I will just have to get around this by using a slower code. How do I switch off SSE4.1 and use a different CPU optimization scheme? Regards, Guanglei On Tue, Sep 3, 2013 at 2:39 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/3/13 1:47 PM, Guanglei Cui wrote: Dear GMX users, I'm attempting to compile gromacs 4.6.3 with an older Intel compiler (ver 11.x). Here is how I compiled FFTW, ./configure CC=icc F77=ifort CFLAGS=-O3 -gcc --prefix=/tmp/gromacs-4.6.3/**fftw-3.3.3/build-intel-threads --enable-threads --enable-sse2 --with-combined-threads --with-our-malloc16 --enable-float And, here is how I invoked cmake, CC=icc CXX=icpc ../cmake-2.8.11/bin/cmake .. -DGMX_FFT_LIBRARY=fftw3 -DFFTWF_LIBRARY=/tmp/gromacs-**4.6.3/fftw-3.3.3/build-intel-** threads/lib/libfftw3f.a -DFFTWF_INCLUDE_DIR=/tmp/**gromacs-4.6.3/fftw-3.3.3/** build-intel-threads/include -DBUILD_SHARED_LIBS=no -DCMAKE_INSTALL_PREFIX=/home/**gc603449/APPLICATIONS/gromac-** 4.6.3/thread-float-static -DREGRESSIONTEST_PATH=/tmp/**gromacs-4.6.3/regressiontests-**4.6.1 When I ran 'make check', 39 out of 142 kernel tests failed, and 2 out of 9 free energy tests failed. This is my first time to compile gromacs, which I am not very familiar with. I wonder if anyone can kindly point out what has gone wrong, and where to look for hints. Any help is much appreciated. Best regards, -- Guanglei Cui PS: I am aware of a warning about using older Intel compilers with 4.6.3, but that's the only quality compiler I got. The gcc compiler I have access to is too old (ver 4.1.x) I assume what you're referring to is http://redmine.gromacs.org/** issues/1126 http://redmine.gromacs.org/issues/1126, so it should be pretty clear (and cmake reminds you) that there are expected regression test failures with this compiler and SSE4.1. I suppose a workaround is to use a different CPU acceleration, but you'll pay a price in performance. Outdated compilers can't be expected to handle all the best features Gromacs has to offer :) -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 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Guanglei Cui -- 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] Steered MD in gromacs
Also, why in vacuo? At least turn on an implicit solvent model. Gianluca On Tue, 3 Sep 2013, Justin Lemkul wrote: On 9/3/13 11:22 AM, hanna pdb wrote: Dear all, I am just starting MD simulations and wanted to see how to perform steered molecular dynamics in gromacs . Most papers and tutorials that I found were done in NAMD. Can anyone recommend examples that were done in gromacs? In my case the tutorial Pull Code and Umbrella Sampling on the gromacs website seems not applicable. I simply want to see how to perform an in vacuo simulation by pulling. Indeed, my tutorial will go beyond what you want, but I don't see how it's not applicable. There is discussion of how to use all (or at least most) of the pull settings and produce a SMD trajectory as part of the protocol. -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 - Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.washington.edu/ Research Scientist at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. http://healthynaturalbaby.org - -- 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 4.6.3 and Intel compiiler 11.x
Hi Mark, I agree with you and Justin, but let's just say there are things that are out of my control ;-) I just tried SSE2 and NONE. Both failed the regression check. I think I've spent enough time on this, which justifies escalating this to someone with the control, but is failing regression check with no CPU/instruction optimization normal? Regards, Guanglei On Tue, Sep 3, 2013 at 3:35 PM, Mark Abraham mark.j.abra...@gmail.comwrote: On Tue, Sep 3, 2013 at 7:47 PM, Guanglei Cui amber.mail.arch...@gmail.com wrote: Dear GMX users, I'm attempting to compile gromacs 4.6.3 with an older Intel compiler (ver 11.x). Here is how I compiled FFTW, ./configure CC=icc F77=ifort CFLAGS=-O3 -gcc --prefix=/tmp/gromacs-4.6.3/fftw-3.3.3/build-intel-threads --enable-threads --enable-sse2 --with-combined-threads --with-our-malloc16 --enable-float I can't imagine you'll benefit from threaded FFTW, but feel free to try... And, here is how I invoked cmake, CC=icc CXX=icpc ../cmake-2.8.11/bin/cmake .. -DGMX_FFT_LIBRARY=fftw3 -DFFTWF_LIBRARY=/tmp/gromacs-4.6.3/fftw-3.3.3/build-intel-threads/lib/libfftw3f.a -DFFTWF_INCLUDE_DIR=/tmp/gromacs-4.6.3/fftw-3.3.3/build-intel-threads/include -DBUILD_SHARED_LIBS=no -DCMAKE_INSTALL_PREFIX=/home/gc603449/APPLICATIONS/gromac-4.6.3/thread-float-static -DREGRESSIONTEST_PATH=/tmp/gromacs-4.6.3/regressiontests-4.6.1 When I ran 'make check', 39 out of 142 kernel tests failed, and 2 out of 9 free energy tests failed. This is my first time to compile gromacs, which I am not very familiar with. I wonder if anyone can kindly point out what has gone wrong, and where to look for hints. Any help is much appreciated. As Justin said, get an up-to-date compiler. gcc regularly outperforms icc, anyway. You can use cmake -DGMX_CPU_ACCELERATION=SSE2 to get a least-common-denominator build, but if you care about threaded FFTW then you care enough to get a new compiler! Mark Best regards, -- Guanglei Cui PS: I am aware of a warning about using older Intel compilers with 4.6.3, but that's the only quality compiler I got. The gcc compiler I have access to is too old (ver 4.1.x) -- 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 -- Guanglei Cui -- 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 4.6.3 and Intel compiiler 11.x
Can't be sure - we don't know what the problem with the compiler *is*. Mark On Tue, Sep 3, 2013 at 9:50 PM, Guanglei Cui amber.mail.arch...@gmail.com wrote: Hi Mark, I agree with you and Justin, but let's just say there are things that are out of my control ;-) I just tried SSE2 and NONE. Both failed the regression check. I think I've spent enough time on this, which justifies escalating this to someone with the control, but is failing regression check with no CPU/instruction optimization normal? Regards, Guanglei On Tue, Sep 3, 2013 at 3:35 PM, Mark Abraham mark.j.abra...@gmail.comwrote: On Tue, Sep 3, 2013 at 7:47 PM, Guanglei Cui amber.mail.arch...@gmail.com wrote: Dear GMX users, I'm attempting to compile gromacs 4.6.3 with an older Intel compiler (ver 11.x). Here is how I compiled FFTW, ./configure CC=icc F77=ifort CFLAGS=-O3 -gcc --prefix=/tmp/gromacs-4.6.3/fftw-3.3.3/build-intel-threads --enable-threads --enable-sse2 --with-combined-threads --with-our-malloc16 --enable-float I can't imagine you'll benefit from threaded FFTW, but feel free to try... And, here is how I invoked cmake, CC=icc CXX=icpc ../cmake-2.8.11/bin/cmake .. -DGMX_FFT_LIBRARY=fftw3 -DFFTWF_LIBRARY=/tmp/gromacs-4.6.3/fftw-3.3.3/build-intel-threads/lib/libfftw3f.a -DFFTWF_INCLUDE_DIR=/tmp/gromacs-4.6.3/fftw-3.3.3/build-intel-threads/include -DBUILD_SHARED_LIBS=no -DCMAKE_INSTALL_PREFIX=/home/gc603449/APPLICATIONS/gromac-4.6.3/thread-float-static -DREGRESSIONTEST_PATH=/tmp/gromacs-4.6.3/regressiontests-4.6.1 When I ran 'make check', 39 out of 142 kernel tests failed, and 2 out of 9 free energy tests failed. This is my first time to compile gromacs, which I am not very familiar with. I wonder if anyone can kindly point out what has gone wrong, and where to look for hints. Any help is much appreciated. As Justin said, get an up-to-date compiler. gcc regularly outperforms icc, anyway. You can use cmake -DGMX_CPU_ACCELERATION=SSE2 to get a least-common-denominator build, but if you care about threaded FFTW then you care enough to get a new compiler! Mark Best regards, -- Guanglei Cui PS: I am aware of a warning about using older Intel compilers with 4.6.3, but that's the only quality compiler I got. The gcc compiler I have access to is too old (ver 4.1.x) -- 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 -- Guanglei Cui -- 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] gromacs 4.6.3 and Intel compiiler 11.x
On Tue, Sep 3, 2013 at 9:50 PM, Guanglei Cui amber.mail.arch...@gmail.com wrote: Hi Mark, I agree with you and Justin, but let's just say there are things that are out of my control ;-) I just tried SSE2 and NONE. Both failed the regression check. That's alarming, with GMX_CPU_ACCELERATION=None only the plain C kernels get compiled which should pass the regressiontests even with icc 11 - although I have not tried myself. Some things that don't take much time and may be useful to try: - make sure that when GMX_CPU_ACCELERATION=None the resulting binary does not get compiled with flags that instruct the compiler to auto-generate SSE4.1 code (e.g. -msse4.1 or -xHOST); - run with the GMX_NOOPTIMIZEDKERNELS environment variable set which disables the architecture-specific kernels at runtime (regardless of what mdrun was compiled with); the end result should be the same as above: the plain C kernels should be used (although with GMX_CPU_ACCELERATION != None the instructions of requested instruction set will be generated by the compiler as an optimization). -- Szilárd I think I've spent enough time on this, which justifies escalating this to someone with the control, but is failing regression check with no CPU/instruction optimization normal? Regards, Guanglei On Tue, Sep 3, 2013 at 3:35 PM, Mark Abraham mark.j.abra...@gmail.comwrote: On Tue, Sep 3, 2013 at 7:47 PM, Guanglei Cui amber.mail.arch...@gmail.com wrote: Dear GMX users, I'm attempting to compile gromacs 4.6.3 with an older Intel compiler (ver 11.x). Here is how I compiled FFTW, ./configure CC=icc F77=ifort CFLAGS=-O3 -gcc --prefix=/tmp/gromacs-4.6.3/fftw-3.3.3/build-intel-threads --enable-threads --enable-sse2 --with-combined-threads --with-our-malloc16 --enable-float I can't imagine you'll benefit from threaded FFTW, but feel free to try... And, here is how I invoked cmake, CC=icc CXX=icpc ../cmake-2.8.11/bin/cmake .. -DGMX_FFT_LIBRARY=fftw3 -DFFTWF_LIBRARY=/tmp/gromacs-4.6.3/fftw-3.3.3/build-intel-threads/lib/libfftw3f.a -DFFTWF_INCLUDE_DIR=/tmp/gromacs-4.6.3/fftw-3.3.3/build-intel-threads/include -DBUILD_SHARED_LIBS=no -DCMAKE_INSTALL_PREFIX=/home/gc603449/APPLICATIONS/gromac-4.6.3/thread-float-static -DREGRESSIONTEST_PATH=/tmp/gromacs-4.6.3/regressiontests-4.6.1 When I ran 'make check', 39 out of 142 kernel tests failed, and 2 out of 9 free energy tests failed. This is my first time to compile gromacs, which I am not very familiar with. I wonder if anyone can kindly point out what has gone wrong, and where to look for hints. Any help is much appreciated. As Justin said, get an up-to-date compiler. gcc regularly outperforms icc, anyway. You can use cmake -DGMX_CPU_ACCELERATION=SSE2 to get a least-common-denominator build, but if you care about threaded FFTW then you care enough to get a new compiler! Mark Best regards, -- Guanglei Cui PS: I am aware of a warning about using older Intel compilers with 4.6.3, but that's the only quality compiler I got. The gcc compiler I have access to is too old (ver 4.1.x) -- 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 -- Guanglei Cui -- 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] gromacs 4.6.3 and Intel compiiler 11.x
On Tue, Sep 3, 2013 at 7:47 PM, Guanglei Cui amber.mail.arch...@gmail.com wrote: Dear GMX users, I'm attempting to compile gromacs 4.6.3 with an older Intel compiler (ver 11.x). Here is how I compiled FFTW, ./configure CC=icc F77=ifort CFLAGS=-O3 -gcc --prefix=/tmp/gromacs-4.6.3/fftw-3.3.3/build-intel-threads --enable-threads --enable-sse2 --with-combined-threads --with-our-malloc16 --enable-float I can't imagine you'll benefit from threaded FFTW, but feel free to try... And, here is how I invoked cmake, CC=icc CXX=icpc ../cmake-2.8.11/bin/cmake .. -DGMX_FFT_LIBRARY=fftw3 -DFFTWF_LIBRARY=/tmp/gromacs-4.6.3/fftw-3.3.3/build-intel-threads/lib/libfftw3f.a -DFFTWF_INCLUDE_DIR=/tmp/gromacs-4.6.3/fftw-3.3.3/build-intel-threads/include -DBUILD_SHARED_LIBS=no -DCMAKE_INSTALL_PREFIX=/home/gc603449/APPLICATIONS/gromac-4.6.3/thread-float-static -DREGRESSIONTEST_PATH=/tmp/gromacs-4.6.3/regressiontests-4.6.1 When I ran 'make check', 39 out of 142 kernel tests failed, and 2 out of 9 free energy tests failed. This is my first time to compile gromacs, which I am not very familiar with. I wonder if anyone can kindly point out what has gone wrong, and where to look for hints. Any help is much appreciated. As Justin said, get an up-to-date compiler. gcc regularly outperforms icc, anyway. You can use cmake -DGMX_CPU_ACCELERATION=SSE2 to get a least-common-denominator build, but if you care about threaded FFTW then you care enough to get a new compiler! Mark Best regards, -- Guanglei Cui PS: I am aware of a warning about using older Intel compilers with 4.6.3, but that's the only quality compiler I got. The gcc compiler I have access to is too old (ver 4.1.x) -- 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] Steered MD in gromacs
On 9/3/13 3:10 PM, Gianluca Interlandi wrote: Also, why in vacuo? At least turn on an implicit solvent model. I can think of reasons to study molecular interactions in vacuo via pulling. Why is solvent (explicit or implicit) an absolute requirement? -Justin On Tue, 3 Sep 2013, Justin Lemkul wrote: On 9/3/13 11:22 AM, hanna pdb wrote: Dear all, I am just starting MD simulations and wanted to see how to perform steered molecular dynamics in gromacs . Most papers and tutorials that I found were done in NAMD. Can anyone recommend examples that were done in gromacs? In my case the tutorial Pull Code and Umbrella Sampling on the gromacs website seems not applicable. I simply want to see how to perform an in vacuo simulation by pulling. Indeed, my tutorial will go beyond what you want, but I don't see how it's not applicable. There is discussion of how to use all (or at least most) of the pull settings and produce a SMD trajectory as part of the protocol. -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 - Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.washington.edu/ Research Scientist at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. http://healthynaturalbaby.org - -- == 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] fluctuation of energy in rerun
Hello I am running a simulation with charge and without charge for 128 pairs of bmim-tf2n ioinc liquids. This is the command for the original run without charge mdrun -s gs.tpr -o gs.trr -c 0.pdb -e gs.edr -g gs.log -pd -nt 8 This is the command for the rerun with charge mdrun -s es.tpr -o es.trr -c 0.pdb -e es.edr -g es.log -rerun gs.trr -pd -nt 8 In the original trajectory, the energy of the system fluctuates around 5000 kJ/mol. In the rerun trajectory, the energy of the system also mostly fluctuates around 5000 kJ/mol, but sometimes it jumps to 10^13 or 10^-13. In the most recent run (20 ns), 16 data points out of 200 were extremely large. Checking the trajectory files, it seems like caused by molecule stretching across the pbc. Nilesh -- 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] Steered MD in gromacs
On 9/3/13 3:10 PM, Gianluca Interlandi wrote: Also, why in vacuo? At least turn on an implicit solvent model. I can think of reasons to study molecular interactions in vacuo via pulling. I'm sure there are. G Why is solvent (explicit or implicit) an absolute requirement? -Justin On Tue, 3 Sep 2013, Justin Lemkul wrote: On 9/3/13 11:22 AM, hanna pdb wrote: Dear all, I am just starting MD simulations and wanted to see how to perform steered molecular dynamics in gromacs . Most papers and tutorials that I found were done in NAMD. Can anyone recommend examples that were done in gromacs? In my case the tutorial Pull Code and Umbrella Sampling on the gromacs website seems not applicable. I simply want to see how to perform an in vacuo simulation by pulling. Indeed, my tutorial will go beyond what you want, but I don't see how it's not applicable. There is discussion of how to use all (or at least most) of the pull settings and produce a SMD trajectory as part of the protocol. -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 - Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.washington.edu/ Research Scientist at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. http://healthynaturalbaby.org - -- == 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 - Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.washington.edu/ Research Scientist at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. http://healthynaturalbaby.org - -- 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] Re: MD vs. free energy simulations
On 9/2/13 9:43 PM, Jernej Zidar wrote: Dear Justin, I set the couple_intramol parameter to yes and rerun the free energy simulations. mdrun was able to fully utilize all the cores in the system but there's one issue. The free energy of solvation is vastly different if the parameter is set to 'no' (DG=-408.10 +/- 8.69 kJ/mol) or 'yes' (1890.14 +/- 15.52). The behavior observed in the simulations is more consistent with the latter number. The latter number, of course, is not an actual final answer. You have to do a corresponding gas-phase calculation to determine the real DG of solvation. I see. I'll do a gas-phase calculation as well. The manual states that 'yes' can be used can be useful for partitioning free-energies of relatively large molecules, where the intra-molecular non-bonded interactions might lead to kinetically trapped vacuum conformations. The 1-4 pair interactions are not turned off. My molecule has 161 atoms. How large is relatively large ? I think a bigger factor is flexibility. For a relatively rigid, conjugated system, it may not be a big issue. Gut feeling? Yes, I'd say that something with 161 atoms is relatively large. The polymer molecules is indeed very flexible. -- 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] parameters for Hem ligated with co
Dear all, Can anyone please share your heme ligated to CO ligand parameters? There is a parameters file exist in charmm22 and gromos but they are not well defined. It would be really appreciated if you anyone share here. Thanks. -- 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 4.6.3 and Intel compiiler 11.x
Hi Szilard, Thanks for your reply. I may try your suggestions tomorrow when I get back to work. Feeling curious, I downloaded and compiled gmx 4.6.3 on my home computer (gcc-4.6.3 and ubuntu 12.04). Even with the default (below), kernel (38 out of 142) and freeenergy (2 out of 9) tests would still fail. I'm not sure what is going on. Perhaps I should try an earlier version that matches the regressiontests? cmake .. -DGMX_BUILD_OWN_FFTW=on -DREGRESSIONTEST_PATH=/home/cuigl/Downloads/regressiontests-4.6.1 Regards, Guanglei On Tue, Sep 3, 2013 at 7:40 PM, Szilárd Páll szilard.p...@cbr.su.se wrote: On Tue, Sep 3, 2013 at 9:50 PM, Guanglei Cui amber.mail.arch...@gmail.com wrote: Hi Mark, I agree with you and Justin, but let's just say there are things that are out of my control ;-) I just tried SSE2 and NONE. Both failed the regression check. That's alarming, with GMX_CPU_ACCELERATION=None only the plain C kernels get compiled which should pass the regressiontests even with icc 11 - although I have not tried myself. Some things that don't take much time and may be useful to try: - make sure that when GMX_CPU_ACCELERATION=None the resulting binary does not get compiled with flags that instruct the compiler to auto-generate SSE4.1 code (e.g. -msse4.1 or -xHOST); - run with the GMX_NOOPTIMIZEDKERNELS environment variable set which disables the architecture-specific kernels at runtime (regardless of what mdrun was compiled with); the end result should be the same as above: the plain C kernels should be used (although with GMX_CPU_ACCELERATION != None the instructions of requested instruction set will be generated by the compiler as an optimization). -- Szilárd I think I've spent enough time on this, which justifies escalating this to someone with the control, but is failing regression check with no CPU/instruction optimization normal? Regards, Guanglei On Tue, Sep 3, 2013 at 3:35 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Tue, Sep 3, 2013 at 7:47 PM, Guanglei Cui amber.mail.arch...@gmail.com wrote: Dear GMX users, I'm attempting to compile gromacs 4.6.3 with an older Intel compiler (ver 11.x). Here is how I compiled FFTW, ./configure CC=icc F77=ifort CFLAGS=-O3 -gcc --prefix=/tmp/gromacs-4.6.3/fftw-3.3.3/build-intel-threads --enable-threads --enable-sse2 --with-combined-threads --with-our-malloc16 --enable-float I can't imagine you'll benefit from threaded FFTW, but feel free to try... And, here is how I invoked cmake, CC=icc CXX=icpc ../cmake-2.8.11/bin/cmake .. -DGMX_FFT_LIBRARY=fftw3 -DFFTWF_LIBRARY=/tmp/gromacs-4.6.3/fftw-3.3.3/build-intel-threads/lib/libfftw3f.a -DFFTWF_INCLUDE_DIR=/tmp/gromacs-4.6.3/fftw-3.3.3/build-intel-threads/include -DBUILD_SHARED_LIBS=no -DCMAKE_INSTALL_PREFIX=/home/gc603449/APPLICATIONS/gromac-4.6.3/thread-float-static -DREGRESSIONTEST_PATH=/tmp/gromacs-4.6.3/regressiontests-4.6.1 When I ran 'make check', 39 out of 142 kernel tests failed, and 2 out of 9 free energy tests failed. This is my first time to compile gromacs, which I am not very familiar with. I wonder if anyone can kindly point out what has gone wrong, and where to look for hints. Any help is much appreciated. As Justin said, get an up-to-date compiler. gcc regularly outperforms icc, anyway. You can use cmake -DGMX_CPU_ACCELERATION=SSE2 to get a least-common-denominator build, but if you care about threaded FFTW then you care enough to get a new compiler! Mark Best regards, -- Guanglei Cui PS: I am aware of a warning about using older Intel compilers with 4.6.3, but that's the only quality compiler I got. The gcc compiler I have access to is too old (ver 4.1.x) -- 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 -- Guanglei Cui -- 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. *
