Re: [gmx-users] gromacs on GPU
As I understood that gromacs version already has included openMM so the installation of the external openMM sources is not needed, isnt it ? also I wounder to know what exactly CUDA version is needed ? For example I've tried lattest cuda-5.0 but with that version i've obtain error from mdrun-openmm that platform cuda was not detected (gromacs was compilated without any errors). I've seen that erorr in other posts in the mailing list but could not found any possible sollutions. by the way is it possible to compilate gromacs-4.6 agains other platgorm ( e.g openCL) ? I have no problems with the compatibility of the openCL and openMM. James 2013/1/9 Szilárd Páll szilard.p...@cbr.su.se: On Tue, Jan 8, 2013 at 3:22 PM, James Starlight jmsstarli...@gmail.comwrote: So could someone provide me more about gpu-accelerated MD implemented in the 4.6 gromacs ? Does it require openMM (what version is supported FYI, if nobody can, trust G: http://lmgtfy.com/?q=gromacs+4.6+gpu+acceleration http://lmgtfy.com/?q=gromacs+4.6+installation+instructions The wiki and mailing list contains quite extensive information (indexed by G). Otherwise, release notes (not final): http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x Install guide is at the expected location: http://www.gromacs.org/Documentation/Installation_Instructions Cheers, -- Szilárd for that gromacs release ?) installed? By the way at present time I force with the problem of compilation 4.1.1 openMM (i need to compile openMM because of cuda-5.0 ). If someone have done it (openMM 4.11 +cuda 5.0 + gromacs-4.5 for lattest geforces) please let me know. James 2013/1/7 James Starlight jmsstarli...@gmail.com: Hi Szilárd! As I understood you correctly gromacs-4.6 have specific algorithm (independent on openMM?) for gpu-based calculations havent ? If it true how I should compilate such new gpu-based gromacs? In the gromacs-4.6-beta-3 folder I've found instructuon for the standart installation via cmake cmake PATH_TO_SOURCE_DIRECTORY -DGMX_OPENMM=ON -DGMX_THREADS=OFF James 2013/1/7 Szilárd Páll szilard.p...@cbr.su.se: Szilárd -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] system not equilibrated
Hi all, I ran energy minimization (em) step, (protein-CNT in water) by these conditions: title = Minimization integrator = steep emtol = 1000.0 emstep = 0.01 nsteps = 15 energygrps = Protein CNT nstlist = 1 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 rvdw = 1.0 pbc = xyz but when it recieves to 4 step (nearly), it gives error: Step= 125, Dmax= 7.8e-06 nm, Epot= -1.79432e+07 Fmax= 8.35837e+04, atom= 10656 Step= 129, Dmax= 1.2e-06 nm, Epot= -1.79432e+07 Fmax= 8.35979e+04, atom= 10656 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. writing lowest energy coordinates. Back Off! I just backed up em2.gro to ./#em2.gro.1# Steepest Descents converged to machine precision in 130 steps, but did not reach the requested Fmax 1000. Potential Energy = -1.7943236e+07 Maximum force = 8.3583656e+04 on atom 10656 Norm of force = 2.1333945e+03 then I ran my system with emtol=10 , but the error repeated too. then I ran it by double-precision , but was not successful too. 1- I changed fmax value only in .mdp file, is it correct? or I should change any parameter in topology file? 2- is the nsteps too much ?and problem is long time?what is its problem? please guide me tnx Niki -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] gromacs on GPU
I've solved previous problem but havent been able to launch mdrun-openmm. Below you can find mdrun's output Back Off! I just backed up md_test.log to ./#md_test.log.3# Reading file md_test.tpr, VERSION 4.6-beta3 (single precision) Changing nstlist from 10 to 40, rlist from 1 to 1.146 Compiled acceleration: None (Gromacs could use AVX_256 on this machine, which is better) 1 GPU detected: #0: NVIDIA GeForce GTX 670, compute cap.: 3.0, ECC: no, stat: compatible 1 GPU auto-selected to be used for this run: #0 Program mdrun-openmm, VERSION 4.6-beta3 Source code file: /home/own/gromacs-4.6-beta3/src/kernel/openmm_wrapper.cpp, line: 1367 Fatal error: OpenMM exception caught while initializating: Error setting device flags cannot set while device is active in this process For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I'm still using cuda-5-toolkit with the 304.54 driver. Also my question about openCL is still valid. I've browesed manual but didnt found how I can compile gromacs with openCL instead of Cuda. On openMM group developers told me that openCL would give much performance for gpu-accelerated simulation in comparison to the CUDA. James 2013/1/9 James Starlight jmsstarli...@gmail.com: As I understood that gromacs version already has included openMM so the installation of the external openMM sources is not needed, isnt it ? also I wounder to know what exactly CUDA version is needed ? For example I've tried lattest cuda-5.0 but with that version i've obtain error from mdrun-openmm that platform cuda was not detected (gromacs was compilated without any errors). I've seen that erorr in other posts in the mailing list but could not found any possible sollutions. by the way is it possible to compilate gromacs-4.6 agains other platgorm ( e.g openCL) ? I have no problems with the compatibility of the openCL and openMM. James 2013/1/9 Szilárd Páll szilard.p...@cbr.su.se: On Tue, Jan 8, 2013 at 3:22 PM, James Starlight jmsstarli...@gmail.comwrote: So could someone provide me more about gpu-accelerated MD implemented in the 4.6 gromacs ? Does it require openMM (what version is supported FYI, if nobody can, trust G: http://lmgtfy.com/?q=gromacs+4.6+gpu+acceleration http://lmgtfy.com/?q=gromacs+4.6+installation+instructions The wiki and mailing list contains quite extensive information (indexed by G). Otherwise, release notes (not final): http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x Install guide is at the expected location: http://www.gromacs.org/Documentation/Installation_Instructions Cheers, -- Szilárd for that gromacs release ?) installed? By the way at present time I force with the problem of compilation 4.1.1 openMM (i need to compile openMM because of cuda-5.0 ). If someone have done it (openMM 4.11 +cuda 5.0 + gromacs-4.5 for lattest geforces) please let me know. James 2013/1/7 James Starlight jmsstarli...@gmail.com: Hi Szilárd! As I understood you correctly gromacs-4.6 have specific algorithm (independent on openMM?) for gpu-based calculations havent ? If it true how I should compilate such new gpu-based gromacs? In the gromacs-4.6-beta-3 folder I've found instructuon for the standart installation via cmake cmake PATH_TO_SOURCE_DIRECTORY -DGMX_OPENMM=ON -DGMX_THREADS=OFF James 2013/1/7 Szilárd Páll szilard.p...@cbr.su.se: Szilárd -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] system not equilibrated
On 1/9/13 3:41 AM, Gmx Niki wrote: Hi all, I ran energy minimization (em) step, (protein-CNT in water) by these conditions: title= Minimization integrator= steep emtol= 1000.0 emstep = 0.01 nsteps= 15 energygrps= Protein CNT nstlist= 1 ns_type= grid rlist= 1.0 coulombtype= PME rcoulomb= 1.0 rvdw= 1.0 pbc= xyz but when it recieves to 4 step (nearly), it gives error: Step= 125, Dmax= 7.8e-06 nm, Epot= -1.79432e+07 Fmax= 8.35837e+04, atom= 10656 Step= 129, Dmax= 1.2e-06 nm, Epot= -1.79432e+07 Fmax= 8.35979e+04, atom= 10656 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. writing lowest energy coordinates. Back Off! I just backed up em2.gro to ./#em2.gro.1# Steepest Descents converged to machine precision in 130 steps, but did not reach the requested Fmax 1000. Potential Energy = -1.7943236e+07 Maximum force = 8.3583656e+04 on atom 10656 Norm of force = 2.1333945e+03 then I ran my system with emtol=10 , but the error repeated too. then I ran it by double-precision , but was not successful too. 1- I changed fmax value only in .mdp file, is it correct? or I should change any parameter in topology file? 2- is the nsteps too much ?and problem is long time?what is its problem? You have a maximum force on the order of 10^4, which is an order of magnitude higher than what you initially requested. mdrun is telling you that the problem is focused on atom 10656. Open up your structure in your visualization software of choice and find that atom. You likely have some unresolved clashes there that are causing this problem. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] force field for GPI ligands which has lipid and carbohydrates ?
On 1/9/13 2:48 AM, 라지브간디 wrote: Could you tell me which force field recognizes the GPI ligand which posses lipid and mannose which interacts with protein? Probably none do by default, but suitable parameters may exist within the literature or with a Google search. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] repost_hybrid imlicit/explicit solvent
Hi this is a repost, maybe it was missed. I want to create a system with hybrid solvent (explicit/implicit). My system is large enough to calculate it with explicit SOL. But it is critical to study the behavior of several water molecules in the site. The idea is to generate a layer of explicit water molecules around the protein molecule with ligand in the binding site and than fill the box with continuous imlicit solvent with epsilon = 80. To prevent the departure of discrete water molecules into the implicit layer I want to limit the distance of their movement with something like PULL COM distance or anything else. Is it real or I have to find another way or choose another software for this purpose. Thank you in advance -- * Nemo me impune lacessit* -- 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] Toy input system - MD simulation
Hello, I am new at this and I am working with the constraints algorithms used in a MD simulation. I would like to now how they work, what type of coordinates they use and also to identify some variables. For that, I am trying to do a simulation with a toy input system, like methane or ethane but I am having some troubles: I started with a methane PDB file and pdb2gmx but I got errors, I tried with a ethane simulation using the files: ethane.gro, ethane.mdp and ethane.top but I also got errors, ... I know it is a very open-question but, could you help me? What would you recommend me? Do you have a toy input system? Thank you very much, Maria -- 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] repost_hybrid imlicit/explicit solvent
On 1/9/13 6:02 AM, Алексей Раевский wrote: Hi this is a repost, maybe it was missed. I want to create a system with hybrid solvent (explicit/implicit). My system is large enough to calculate it with explicit SOL. But it is critical to study the behavior of several water molecules in the site. The idea is to generate a layer of explicit water molecules around the protein molecule with ligand in the binding site and than fill the box with continuous imlicit solvent with epsilon = 80. To prevent the departure of discrete water molecules into the implicit layer I want to limit the distance of their movement with something like PULL COM distance or anything else. Is it real or I have to find another way or choose another software for this purpose. Perhaps something like a spherical restraint would be more useful than the pull code, as was done in http://www.pnas.org/content/108/17/6838. The spherical restraint potential has been implemented in the master development branch, and thus won't appear in the next release (4.6) but perhaps you can easily patch the source to use this feature. I have no idea how that will play with an external implicit environment, but it's probably worth a shot. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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)
Dear Justin first ,I get error on atom number . after change emtol to 10 , I get same error on atom number . what' your idea? how to solve it? I use this file for PR step , but I get this error: A charge group moved too far between two domain decomposition your system might be not equilibrated well enough my system without charge (total charge is zero) what' your idea? 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] (no subject)
On 1/9/13 8:57 AM, sara azhari wrote: Dear Justin first ,I get error on atom number . after change emtol to 10 , I get same error on atom number . what' your idea? how to solve it? mdrun probably did a different number of steps and/or moved through configurations different. The bottom line is there is something wrong with whatever coordinates you are providing it such that the minimization cannot be successfully finished. I use this file for PR step , but I get this error: Proceeding when a simple energy minimization has failed is futile. Your system is far too unstable for a simulation. -Justin A charge group moved too far between two domain decomposition your system might be not equilibrated well enough my system without charge (total charge is zero) what' your idea? thanks -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Toy input system - MD simulation
On 1/9/13 6:25 AM, Maria Astón Serrano wrote: Hello, I am new at this and I am working with the constraints algorithms used in a MD simulation. I would like to now how they work, what type of coordinates they use and also to identify some variables. For that, I am trying to do a simulation with a toy input system, like methane or ethane but I am having some troubles: I started with a methane PDB file and pdb2gmx but I got errors, I tried with a ethane simulation using the files: ethane.gro, ethane.mdp and ethane.top but I also got errors, ... I know it is a very open-question but, could you help me? What would you recommend me? Do you have a toy input system? You can find a large number of common molecules (both coordinates and topologies) on http://virtualchemistry.org/. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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: system not equilibrated
Hi all, I ran energy minimization (em) step, (protein-CNT in water) by these conditions: title = Minimization integrator = steep emtol = 1000.0 emstep = 0.01 nsteps = 15 energygrps = Protein CNT nstlist = 1 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 rvdw = 1.0 pbc = xyz but when it recieves to 4 step (nearly), it gives error: Step= 125, Dmax= 7.8e-06 nm, Epot= -1.79432e+07 Fmax= 8.35837e+04, atom= 10656 Step= 129, Dmax= 1.2e-06 nm, Epot= -1.79432e+07 Fmax= 8.35979e+04, atom= 10656 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. writing lowest energy coordinates. Back Off! I just backed up em2.gro to ./#em2.gro.1# Steepest Descents converged to machine precision in 130 steps, but did not reach the requested Fmax 1000. Potential Energy = -1.7943236e+07 Maximum force = 8.3583656e+04 on atom 10656 Norm of force = 2.1333945e+03 then I ran my system with emtol=10 , but the error repeated too. then I ran it by double-precision , but was not successful too. 1- I changed fmax value only in .mdp file, is it correct? or I should change any parameter in topology file? 2- is the nsteps too much ?and problem is long time?what is its problem? You have a maximum force on the order of 10^4, which is an order of magnitude higher than what you initially requested. mdrun is telling you that the problem is focused on atom 10656. Open up your structure in your visualization software of choice and find that atom. You likely have some unresolved clashes there that are causing this problem. justin Dear Justin first, I get error on atom number . after change emtol to 10 , I get same error on atom number . what' your idea? how to solve it? I use this file for PR step , but I get this error: A charge group moved too far between two domain decomposition your system might be not equilibrated well enough my system without charge (total charge is zero) what' your idea? 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
[gmx-users] Evaporation Free Energy
Dear GMX users, I just wanted to know that it's possible one estimates Gibbs free energy of evaporation via following the solvation free energy scheme? I'm trying to obtain evaporation rate with using the value of G(evap.) for different hydrocarbon molecules at different temperatures. Any advice would be highly appreciated! Best Regards Rasoul -- 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] Floating point exception with mdrun-gpu on CUDA
Hi, I succesfully built the mdrun-gpu on a MacOS MountainLion having one CUDA NVIDIA GeForce GTX 660 platform. When I try to run one of the GPU benchmarks (e.g. dhfr-impl-1nm.bench) a floating point exception occurs. The same happens for all the benchmarks. I have already tested the functionality of the CUDA GPU with the CUDA toolkit samples. Hope someone can help me to understand what is going wrong.. thanks in advance! The last part of the output of mdrun-gpu is as follows: .. -[no]ionize bool no Do a simulation including the effect of an X-Ray bombardment on your system -device string Device option string Reading file topol.tpr, VERSION 4.5.1-dev-20100917-b1d66 (single precision) WARNING: OpenMM does not support leap-frog, will use velocity-verlet integrator. WARNING: OpenMM supports only Andersen thermostat with the md/md-vv/md-vv-avek integrators. WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE and CCMA. Accuracy is based on the SHAKE tolerance set by the shake_tol option. Floating point exception: 8 -- View this message in context: http://gromacs.5086.n6.nabble.com/Floating-point-exception-with-mdrun-gpu-on-CUDA-tp5004393.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
Re: [gmx-users] gromacs on GPU
On Wed, Jan 9, 2013 at 3:17 AM, James Starlight jmsstarli...@gmail.comwrote: As I understood that gromacs version already has included openMM so the installation of the external openMM sources is not needed, isnt it ? No the new build in GPU implementation and openMM are two different things. The Gromacs-OpenMM interface isn't actively maintained and thus not recommended. also I wounder to know what exactly CUDA version is needed ? For example I've tried lattest cuda-5.0 but with that version i've obtain error from mdrun-openmm that platform cuda was not detected (gromacs was compilated without any errors). with the natived gpu implementation (GMX_GPU) cuda 5.0 works fine. by the way is it possible to compilate gromacs-4.6 agains other platgorm ( e.g openCL) ? I have no problems with the compatibility of the openCL and openMM. GMX_GPU doesn't support openCL. Roland James 2013/1/9 Szilárd Páll szilard.p...@cbr.su.se: On Tue, Jan 8, 2013 at 3:22 PM, James Starlight jmsstarli...@gmail.com wrote: So could someone provide me more about gpu-accelerated MD implemented in the 4.6 gromacs ? Does it require openMM (what version is supported FYI, if nobody can, trust G: http://lmgtfy.com/?q=gromacs+4.6+gpu+acceleration http://lmgtfy.com/?q=gromacs+4.6+installation+instructions The wiki and mailing list contains quite extensive information (indexed by G). Otherwise, release notes (not final): http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x Install guide is at the expected location: http://www.gromacs.org/Documentation/Installation_Instructions Cheers, -- Szilárd for that gromacs release ?) installed? By the way at present time I force with the problem of compilation 4.1.1 openMM (i need to compile openMM because of cuda-5.0 ). If someone have done it (openMM 4.11 +cuda 5.0 + gromacs-4.5 for lattest geforces) please let me know. James 2013/1/7 James Starlight jmsstarli...@gmail.com: Hi Szilárd! As I understood you correctly gromacs-4.6 have specific algorithm (independent on openMM?) for gpu-based calculations havent ? If it true how I should compilate such new gpu-based gromacs? In the gromacs-4.6-beta-3 folder I've found instructuon for the standart installation via cmake cmake PATH_TO_SOURCE_DIRECTORY -DGMX_OPENMM=ON -DGMX_THREADS=OFF James 2013/1/7 Szilárd Páll szilard.p...@cbr.su.se: Szilárd -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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] Floating point exception with mdrun-gpu on CUDA
Hi, it seems you are using OpenMM. The recommended approach is to compile with GMX_OPENMM=off and GMX_GPU=on. Roland On Wed, Jan 9, 2013 at 10:45 AM, sdlonga dlo...@caspur.it wrote: Hi, I succesfully built the mdrun-gpu on a MacOS MountainLion having one CUDA NVIDIA GeForce GTX 660 platform. When I try to run one of the GPU benchmarks (e.g. dhfr-impl-1nm.bench) a floating point exception occurs. The same happens for all the benchmarks. I have already tested the functionality of the CUDA GPU with the CUDA toolkit samples. Hope someone can help me to understand what is going wrong.. thanks in advance! The last part of the output of mdrun-gpu is as follows: .. -[no]ionize bool no Do a simulation including the effect of an X-Ray bombardment on your system -device string Device option string Reading file topol.tpr, VERSION 4.5.1-dev-20100917-b1d66 (single precision) WARNING: OpenMM does not support leap-frog, will use velocity-verlet integrator. WARNING: OpenMM supports only Andersen thermostat with the md/md-vv/md-vv-avek integrators. WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE and CCMA. Accuracy is based on the SHAKE tolerance set by the shake_tol option. Floating point exception: 8 -- View this message in context: http://gromacs.5086.n6.nabble.com/Floating-point-exception-with-mdrun-gpu-on-CUDA-tp5004393.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 -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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] Floating point exception with mdrun-gpu on CUDA
On 1/9/13 10:54 AM, Roland Schulz wrote: Hi, it seems you are using OpenMM. The recommended approach is to compile with GMX_OPENMM=off and GMX_GPU=on. ...with version 4.6beta3. The version shown is an outdated development version from the 4.5.1 era. OpenMM was the only choice at that point for running on GPU, unless I'm mistaken. Whatever the case, it's probably better for the OP to be using a more current version of the software. -Justin On Wed, Jan 9, 2013 at 10:45 AM, sdlonga dlo...@caspur.it wrote: Hi, I succesfully built the mdrun-gpu on a MacOS MountainLion having one CUDA NVIDIA GeForce GTX 660 platform. When I try to run one of the GPU benchmarks (e.g. dhfr-impl-1nm.bench) a floating point exception occurs. The same happens for all the benchmarks. I have already tested the functionality of the CUDA GPU with the CUDA toolkit samples. Hope someone can help me to understand what is going wrong.. thanks in advance! The last part of the output of mdrun-gpu is as follows: .. -[no]ionize bool no Do a simulation including the effect of an X-Ray bombardment on your system -device string Device option string Reading file topol.tpr, VERSION 4.5.1-dev-20100917-b1d66 (single precision) WARNING: OpenMM does not support leap-frog, will use velocity-verlet integrator. WARNING: OpenMM supports only Andersen thermostat with the md/md-vv/md-vv-avek integrators. WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE and CCMA. Accuracy is based on the SHAKE tolerance set by the shake_tol option. Floating point exception: 8 -- View this message in context: http://gromacs.5086.n6.nabble.com/Floating-point-exception-with-mdrun-gpu-on-CUDA-tp5004393.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 -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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: repost_hybrid imlicit/explicit solvent
Thank you very much! A lot of users will thank you! -- View this message in context: http://gromacs.5086.n6.nabble.com/repost-hybrid-imlicit-explicit-solvent-tp5004383p5004397.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] Re: hybrid solvent model
look through the answer on my repost today. Maybe we can do it together? -- View this message in context: http://gromacs.5086.n6.nabble.com/hybrid-solvent-model-tp5004347p5004398.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
Re: [gmx-users] energy-mimisation-problem
On 1/9/13 12:20 PM, SANTU BISWAS wrote: dear users, I am performing an energy minimization of apolypeptide(formed by alanine-10-residues) in vacuum box by using Steepest Descent(initially) and then Conjugate Gradient methods in gromacs_4.5.5_doubleprecision.The chain length of alanine-10-mer is around 1.5 nm.Here i want to see only the sort-range interactions.so i use cutoff 2.0 nm .But in the output (.log )file there is a contribution of energy for long-range interactions(in both energy minimisation methods). I do not understand why this is happening. the input file for energy minimisation is, ;title= cpp = /lib/cpp ;include =-I../top/ define = -DFLEXIBLE ; Input file integrator = steep/cg nsteps = 1 nstlist = 1 rlist = 1.0 rcoulomb= 2.0 rvdw= 2.0 ; Energy minimizing stuff emtol = 0.001 emstep = 0.1 nstcgsteep = 10 You haven't set a value for the pbc keyword, so it takes the default value (xyz). The result is that you're not really minimizing in vacuo, but rather in some sort of pseudo-crystal state that probably has lots of periodicity artifacts. That's probably the source of the energy terms - your peptide interacting with itself. -Justin the output(.log )file is, Energies (kJ/mol) Bond AngleProper Dih. Ryckaert-Bell. LJ-14 8.48244e+002.10205e+012.39409e+00 9.86941e+01 1.47894e+02 Coulomb-14LJ (SR)LJ (LR) Coulomb (SR) Coulomb (LR) 1.63221e+03 -1.64038e+02 -4.97232e-01 -3.00455e+03 -1.00138e+01 Potential Pressure (bar) -1.26841e+030.0e+00 santu -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] gromacs on GPU
Roland, indeed the error was that I'have compilate mdrun-openmm which is not the native gpu. now I've made mdrun via cmake CMakeLists.txt -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-5.0 and obtain workable gromacs. My test system consist of calmodulin (charmm27) solvated in tip3p water. total size of the system: 67752 atoms. I have set below values on the mdp file as grompp told me nstlist = 20 cutoff-scheme = Verlet ; !not quite sure whai is this! vdwtype = cut-off Now on the mdrun output I have Using 1 MPI thread Using 4 OpenMP threads 1 GPU detected: #0: NVIDIA GeForce GTX 670, compute cap.: 3.0, ECC: no, stat: compatible 1 GPU auto-selected to be used for this run: #0 does it mean that all 4 cores of my CPU + gpu are used at same time ? is there any other ways to increase performance ? ( e.g I'm not quite sure if open_mpi is used with that build because during compilation cmake asked me only about fftw3 libs). Is there any ways to monitor total performance ( e.g separate cpu and gpu usage ) ? Thanks for suggestions, James 2013/1/9 Roland Schulz rol...@utk.edu: On Wed, Jan 9, 2013 at 3:17 AM, James Starlight jmsstarli...@gmail.comwrote: As I understood that gromacs version already has included openMM so the installation of the external openMM sources is not needed, isnt it ? No the new build in GPU implementation and openMM are two different things. The Gromacs-OpenMM interface isn't actively maintained and thus not recommended. also I wounder to know what exactly CUDA version is needed ? For example I've tried lattest cuda-5.0 but with that version i've obtain error from mdrun-openmm that platform cuda was not detected (gromacs was compilated without any errors). with the natived gpu implementation (GMX_GPU) cuda 5.0 works fine. by the way is it possible to compilate gromacs-4.6 agains other platgorm ( e.g openCL) ? I have no problems with the compatibility of the openCL and openMM. GMX_GPU doesn't support openCL. Roland James 2013/1/9 Szilárd Páll szilard.p...@cbr.su.se: On Tue, Jan 8, 2013 at 3:22 PM, James Starlight jmsstarli...@gmail.com wrote: So could someone provide me more about gpu-accelerated MD implemented in the 4.6 gromacs ? Does it require openMM (what version is supported FYI, if nobody can, trust G: http://lmgtfy.com/?q=gromacs+4.6+gpu+acceleration http://lmgtfy.com/?q=gromacs+4.6+installation+instructions The wiki and mailing list contains quite extensive information (indexed by G). Otherwise, release notes (not final): http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x Install guide is at the expected location: http://www.gromacs.org/Documentation/Installation_Instructions Cheers, -- Szilárd for that gromacs release ?) installed? By the way at present time I force with the problem of compilation 4.1.1 openMM (i need to compile openMM because of cuda-5.0 ). If someone have done it (openMM 4.11 +cuda 5.0 + gromacs-4.5 for lattest geforces) please let me know. James 2013/1/7 James Starlight jmsstarli...@gmail.com: Hi Szilárd! As I understood you correctly gromacs-4.6 have specific algorithm (independent on openMM?) for gpu-based calculations havent ? If it true how I should compilate such new gpu-based gromacs? In the gromacs-4.6-beta-3 folder I've found instructuon for the standart installation via cmake cmake PATH_TO_SOURCE_DIRECTORY -DGMX_OPENMM=ON -DGMX_THREADS=OFF James 2013/1/7 Szilárd Páll szilard.p...@cbr.su.se: Szilárd -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- gmx-users mailing listgmx-users@gromacs.org
Re: [gmx-users] gromacs on GPU
On Wed, Jan 9, 2013 at 9:17 AM, James Starlight jmsstarli...@gmail.comwrote: As I understood that gromacs version already has included openMM so the installation of the external openMM sources is not needed, isnt it ? The manual and wiki guides are meant to be read. Although they are a bit dated, the main body of information is still valid. Please read the documentation; aka RT(F)M: http://www.gromacs.org/gpu#Compiling_and_installation_of_GROMACS-GPU_from_source also I wounder to know what exactly CUDA version is needed ? For example I've tried lattest cuda-5.0 but with that version i've obtain error from mdrun-openmm that platform cuda was not detected (gromacs was compilated without any errors). I've seen that erorr in other posts in the mailing list but could not found any possible sollutions. It surely works with the (admittedly dated) versions the docs suggest, you mileage may vary with other versions, but in principle everything should work with the latest compilers, CUDA, and OpenMM (myself and others have built and ran successfully). by the way is it possible to compilate gromacs-4.6 agains other platgorm ( e.g openCL) ? I have no problems with the compatibility of the openCL and openMM. No, RTM. OpenMM does have an OpenCL plugin, but that's not supported in GROMACS, if you want to use it you'll have to write your own code around the OpenMM library. We have no resources to implement it ATM, but as GROMACS is OSS anyone is welcome to contribute it. And let me reiterate, if you're running explicit solvent you should be using the native GPU acceleration as you've been told before. Cheers, Szilard James 2013/1/9 Szilárd Páll szilard.p...@cbr.su.se: On Tue, Jan 8, 2013 at 3:22 PM, James Starlight jmsstarli...@gmail.com wrote: So could someone provide me more about gpu-accelerated MD implemented in the 4.6 gromacs ? Does it require openMM (what version is supported FYI, if nobody can, trust G: http://lmgtfy.com/?q=gromacs+4.6+gpu+acceleration http://lmgtfy.com/?q=gromacs+4.6+installation+instructions The wiki and mailing list contains quite extensive information (indexed by G). Otherwise, release notes (not final): http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x Install guide is at the expected location: http://www.gromacs.org/Documentation/Installation_Instructions Cheers, -- Szilárd for that gromacs release ?) installed? By the way at present time I force with the problem of compilation 4.1.1 openMM (i need to compile openMM because of cuda-5.0 ). If someone have done it (openMM 4.11 +cuda 5.0 + gromacs-4.5 for lattest geforces) please let me know. James 2013/1/7 James Starlight jmsstarli...@gmail.com: Hi Szilárd! As I understood you correctly gromacs-4.6 have specific algorithm (independent on openMM?) for gpu-based calculations havent ? If it true how I should compilate such new gpu-based gromacs? In the gromacs-4.6-beta-3 folder I've found instructuon for the standart installation via cmake cmake PATH_TO_SOURCE_DIRECTORY -DGMX_OPENMM=ON -DGMX_THREADS=OFF James 2013/1/7 Szilárd Páll szilard.p...@cbr.su.se: Szilárd -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] gromacs on GPU
On Wed, Jan 9, 2013 at 10:27 AM, James Starlight jmsstarli...@gmail.comwrote: I've solved previous problem but havent been able to launch mdrun-openmm. Below you can find mdrun's output Back Off! I just backed up md_test.log to ./#md_test.log.3# Reading file md_test.tpr, VERSION 4.6-beta3 (single precision) Changing nstlist from 10 to 40, rlist from 1 to 1.146 Compiled acceleration: None (Gromacs could use AVX_256 on this machine, which is better) Have you set the CPU acceleration manually to None? If you did *don't* do that, let the build system pick what's best for you. However, if you did not do that, there is some issue with our auto-detection; a log file as a start would possibly help in identifying the issue. 1 GPU detected: #0: NVIDIA GeForce GTX 670, compute cap.: 3.0, ECC: no, stat: compatible 1 GPU auto-selected to be used for this run: #0 Program mdrun-openmm, VERSION 4.6-beta3 Source code file: /home/own/gromacs-4.6-beta3/src/kernel/openmm_wrapper.cpp, line: 1367 Fatal error: OpenMM exception caught while initializating: Error setting device flags cannot set while device is active in this process For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I'm still using cuda-5-toolkit with the 304.54 driver. Also my question about openCL is still valid. I've browesed manual but didnt found how I can compile gromacs with openCL instead of Cuda. On openMM group developers told me that openCL would give much performance for gpu-accelerated simulation in comparison to the CUDA. James 2013/1/9 James Starlight jmsstarli...@gmail.com: As I understood that gromacs version already has included openMM so the installation of the external openMM sources is not needed, isnt it ? also I wounder to know what exactly CUDA version is needed ? For example I've tried lattest cuda-5.0 but with that version i've obtain error from mdrun-openmm that platform cuda was not detected (gromacs was compilated without any errors). I've seen that erorr in other posts in the mailing list but could not found any possible sollutions. by the way is it possible to compilate gromacs-4.6 agains other platgorm ( e.g openCL) ? I have no problems with the compatibility of the openCL and openMM. James 2013/1/9 Szilárd Páll szilard.p...@cbr.su.se: On Tue, Jan 8, 2013 at 3:22 PM, James Starlight jmsstarli...@gmail.com wrote: So could someone provide me more about gpu-accelerated MD implemented in the 4.6 gromacs ? Does it require openMM (what version is supported FYI, if nobody can, trust G: http://lmgtfy.com/?q=gromacs+4.6+gpu+acceleration http://lmgtfy.com/?q=gromacs+4.6+installation+instructions The wiki and mailing list contains quite extensive information (indexed by G). Otherwise, release notes (not final): http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x Install guide is at the expected location: http://www.gromacs.org/Documentation/Installation_Instructions Cheers, -- Szilárd for that gromacs release ?) installed? By the way at present time I force with the problem of compilation 4.1.1 openMM (i need to compile openMM because of cuda-5.0 ). If someone have done it (openMM 4.11 +cuda 5.0 + gromacs-4.5 for lattest geforces) please let me know. James 2013/1/7 James Starlight jmsstarli...@gmail.com: Hi Szilárd! As I understood you correctly gromacs-4.6 have specific algorithm (independent on openMM?) for gpu-based calculations havent ? If it true how I should compilate such new gpu-based gromacs? In the gromacs-4.6-beta-3 folder I've found instructuon for the standart installation via cmake cmake PATH_TO_SOURCE_DIRECTORY -DGMX_OPENMM=ON -DGMX_THREADS=OFF James 2013/1/7 Szilárd Páll szilard.p...@cbr.su.se: Szilárd -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to
Re: [gmx-users] gromacs on GPU
Dear James, On Wed, Jan 9, 2013 at 6:17 PM, James Starlight jmsstarli...@gmail.comwrote: Roland, indeed the error was that I'have compilate mdrun-openmm which is not the native gpu. now I've made mdrun via cmake CMakeLists.txt -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-5.0 and obtain workable gromacs. My test system consist of calmodulin (charmm27) solvated in tip3p water. total size of the system: 67752 atoms. I have set below values on the mdp file as grompp told me nstlist = 20 cutoff-scheme = Verlet ; !not quite sure whai is this! Again RTM: http://www.gromacs.org/Documentation/Cut-off_schemeshttp://www.gromacs.org/Documentation/Cut-off_schemes?highlight=verlet+scheme vdwtype = cut-off Now on the mdrun output I have Using 1 MPI thread Using 4 OpenMP threads 1 GPU detected: #0: NVIDIA GeForce GTX 670, compute cap.: 3.0, ECC: no, stat: compatible 1 GPU auto-selected to be used for this run: #0 does it mean that all 4 cores of my CPU + gpu are used at same time ? Yes. is there any other ways to increase performance ? ( e.g I'm not quite sure if open_mpi is used with that build because during compilation cmake asked me only about fftw3 libs). There could be, but I/we can't well without more information on what and how you compiled and ran. The minimum we need is a log file. Is there any ways to monitor total performance ( e.g separate cpu and gpu usage ) ? See the performance table and summary at the end of the log file. For further CPU monitoring you can use top, for GPUs the nvidia-smi tool that comes together with the driver has some monitoring capabilities. Finally, I would strongly suggest that you check the links I posted in the first mail. There is plenty of documentation and general description on the heterogeneous (CPU+GPU) acceleration on the wiki and mailing list; the google results of the searches I hinted will get you exactly that and more. Let me reiterate: while questions and general interest are appreciated, the *minimum* expectation is that you at least read the relevant part of the documentation and related mailing list posts, especially if this has been already suggested to you. Please do us and yourself a favor and browse through the available resources. Cheers, -- Szilárd Thanks for suggestions, James 2013/1/9 Roland Schulz rol...@utk.edu: On Wed, Jan 9, 2013 at 3:17 AM, James Starlight jmsstarli...@gmail.com wrote: As I understood that gromacs version already has included openMM so the installation of the external openMM sources is not needed, isnt it ? No the new build in GPU implementation and openMM are two different things. The Gromacs-OpenMM interface isn't actively maintained and thus not recommended. also I wounder to know what exactly CUDA version is needed ? For example I've tried lattest cuda-5.0 but with that version i've obtain error from mdrun-openmm that platform cuda was not detected (gromacs was compilated without any errors). with the natived gpu implementation (GMX_GPU) cuda 5.0 works fine. by the way is it possible to compilate gromacs-4.6 agains other platgorm ( e.g openCL) ? I have no problems with the compatibility of the openCL and openMM. GMX_GPU doesn't support openCL. Roland James 2013/1/9 Szilárd Páll szilard.p...@cbr.su.se: On Tue, Jan 8, 2013 at 3:22 PM, James Starlight jmsstarli...@gmail.com wrote: So could someone provide me more about gpu-accelerated MD implemented in the 4.6 gromacs ? Does it require openMM (what version is supported FYI, if nobody can, trust G: http://lmgtfy.com/?q=gromacs+4.6+gpu+acceleration http://lmgtfy.com/?q=gromacs+4.6+installation+instructions The wiki and mailing list contains quite extensive information (indexed by G). Otherwise, release notes (not final): http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x Install guide is at the expected location: http://www.gromacs.org/Documentation/Installation_Instructions Cheers, -- Szilárd for that gromacs release ?) installed? By the way at present time I force with the problem of compilation 4.1.1 openMM (i need to compile openMM because of cuda-5.0 ). If someone have done it (openMM 4.11 +cuda 5.0 + gromacs-4.5 for lattest geforces) please let me know. James 2013/1/7 James Starlight jmsstarli...@gmail.com: Hi Szilárd! As I understood you correctly gromacs-4.6 have specific algorithm (independent on openMM?) for gpu-based calculations havent ? If it true how I should compilate such new gpu-based gromacs? In the gromacs-4.6-beta-3 folder I've found instructuon for the standart installation via cmake cmake PATH_TO_SOURCE_DIRECTORY -DGMX_OPENMM=ON -DGMX_THREADS=OFF James 2013/1/7 Szilárd Páll szilard.p...@cbr.su.se: Szilárd -- gmx-users mailing
Re: [gmx-users] Toy input system - MD simulation
On 2013-01-09 12:25, Maria Astón Serrano wrote: Hello, I am new at this and I am working with the constraints algorithms used in a MD simulation. I would like to now how they work, what type of coordinates they use and also to identify some variables. For that, I am trying to do a simulation with a toy input system, like methane or ethane but I am having some troubles: I started with a methane PDB file and pdb2gmx but I got errors, I tried with a ethane simulation using the files: ethane.gro, ethane.mdp and ethane.top but I also got errors, ... I know it is a very open-question but, could you help me? What would you recommend me? Do you have a toy input system? Thank you very much, Maria http://virtualchemistry.org -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] gromacs on GPU
Dear Szilárd, thanks for help again! 2013/1/9 Szilárd Páll szilard.p...@cbr.su.se: There could be, but I/we can't well without more information on what and how you compiled and ran. The minimum we need is a log file. I've compilated gromacs 4.6-3 beta via simple cmake CMakeLists.txt -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-5.0 make sudo make install I have not added any special params to the grompp or mdrun. After that I've run tested simulation of the calmodulin in explicit water ( 60k atoms ) 100ps and obtain next output Host: starlight pid: 21028 nodeid: 0 nnodes: 1 Gromacs version:VERSION 4.6-beta3 Precision: single MPI library:thread_mpi OpenMP support: enabled GPU support:enabled invsqrt routine:gmx_software_invsqrt(x) CPU acceleration: AVX_256 FFT library:fftw-3.3.2-sse2-avx Large file support: enabled RDTSCP usage: enabled Built on: Wed Jan 9 20:44:51 MSK 2013 Built by: own@starlight [CMAKE] Build OS/arch: Linux 3.2.0-2-amd64 x86_64 Build CPU vendor: GenuineIntel Build CPU brand:Intel(R) Core(TM) i5-3570 CPU @ 3.40GHz Build CPU family: 6 Model: 58 Stepping: 9 Build CPU features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic C compiler: /usr/bin/gcc GNU gcc (Debian 4.6.3-11) 4.6.3 C compiler flags: -mavx -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG C++ compiler: /usr/bin/c++ GNU c++ (Debian 4.6.3-11) 4.6.3 C++ compiler flags: -mavx -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG CUDA compiler: nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2012 NVIDIA Corporation;Built on Fri_Sep_21_17:28:58_PDT_2012;Cuda compilation tools, release 5.0, V0.2.1221 CUDA driver:5.0 CUDA runtime: 5.0 Core t (s) Wall t (s)(%) Time: 2770.700 1051.927 263.4 (ns/day)(hour/ns) Performance:8.2142.922 full log can be found here http://www.sendspace.com/file/inum84 Finally when I check CPU usage I notice that only 1 CPU was full loaded ( 100%) and 2-4 cores were loaded on only 60% but gave me strange results that GPU is not used (I've only monitored temperature of video card and noticed increase of the temperature up to 65 degrees ) +--+ | NVIDIA-SMI 4.304.54 Driver Version: 304.54 | |---+--+--+ | GPU Name | Bus-IdDisp. | Volatile Uncorr. ECC | | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. | |===+==+==| | 0 GeForce GTX 670 | :02:00.0 N/A | N/A | | 38% 63C N/A N/A / N/A | 9% 174MB / 2047MB | N/A Default | +---+--+--+ +-+ | Compute processes: GPU Memory | | GPU PID Process name Usage | |=| |0Not Supported | +-+ Thanks for help again, James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] gromacs on GPU
Hi, is this an implicit water calculation? If so it shouldn't use PME. Roland On Wed, Jan 9, 2013 at 2:27 PM, James Starlight jmsstarli...@gmail.comwrote: Dear Szilárd, thanks for help again! 2013/1/9 Szilárd Páll szilard.p...@cbr.su.se: There could be, but I/we can't well without more information on what and how you compiled and ran. The minimum we need is a log file. I've compilated gromacs 4.6-3 beta via simple cmake CMakeLists.txt -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-5.0 make sudo make install I have not added any special params to the grompp or mdrun. After that I've run tested simulation of the calmodulin in explicit water ( 60k atoms ) 100ps and obtain next output Host: starlight pid: 21028 nodeid: 0 nnodes: 1 Gromacs version:VERSION 4.6-beta3 Precision: single MPI library:thread_mpi OpenMP support: enabled GPU support:enabled invsqrt routine:gmx_software_invsqrt(x) CPU acceleration: AVX_256 FFT library:fftw-3.3.2-sse2-avx Large file support: enabled RDTSCP usage: enabled Built on: Wed Jan 9 20:44:51 MSK 2013 Built by: own@starlight [CMAKE] Build OS/arch: Linux 3.2.0-2-amd64 x86_64 Build CPU vendor: GenuineIntel Build CPU brand:Intel(R) Core(TM) i5-3570 CPU @ 3.40GHz Build CPU family: 6 Model: 58 Stepping: 9 Build CPU features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic C compiler: /usr/bin/gcc GNU gcc (Debian 4.6.3-11) 4.6.3 C compiler flags: -mavx -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG C++ compiler: /usr/bin/c++ GNU c++ (Debian 4.6.3-11) 4.6.3 C++ compiler flags: -mavx -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG CUDA compiler: nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2012 NVIDIA Corporation;Built on Fri_Sep_21_17:28:58_PDT_2012;Cuda compilation tools, release 5.0, V0.2.1221 CUDA driver:5.0 CUDA runtime: 5.0 Core t (s) Wall t (s)(%) Time: 2770.700 1051.927 263.4 (ns/day)(hour/ns) Performance:8.2142.922 full log can be found here http://www.sendspace.com/file/inum84 Finally when I check CPU usage I notice that only 1 CPU was full loaded ( 100%) and 2-4 cores were loaded on only 60% but gave me strange results that GPU is not used (I've only monitored temperature of video card and noticed increase of the temperature up to 65 degrees ) +--+ | NVIDIA-SMI 4.304.54 Driver Version: 304.54 | |---+--+--+ | GPU Name | Bus-IdDisp. | Volatile Uncorr. ECC | | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. | |===+==+==| | 0 GeForce GTX 670 | :02:00.0 N/A | N/A | | 38% 63C N/A N/A / N/A | 9% 174MB / 2047MB | N/A Default | +---+--+--+ +-+ | Compute processes: GPU Memory | | GPU PID Process name Usage | |=| |0Not Supported | +-+ Thanks for help again, James -- 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 -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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] I can't figure out what is wrong with my .gro
Dear all, I created this .gro file following the gromacs format. But when I load it into VMD, it doesn't show the structure or molecule, and I have made many .gro before this one, and learned from many mistakes, but for this one, I don't know what I did wrong. I still proceeded to do simulation anyway and when I do energy minimization, I get an error of infinite normal force and etc (which I read past gmx list question that an atom is severely overlapping and causing the complication). Since I can't even view the .gro structure i made in VMD, I'm going to go ahead and assume there is something wrong with my initial structure to begin with, but I don't know where. Here is the link to my .gro file + topology https://docs.google.com/open?id=0BwQvutOxRUqkNFMtSmVDanlwRFE https://docs.google.com/open?id=0BwQvutOxRUqkRkNQR2RYS0d6aDA https://docs.google.com/open?id=0BwQvutOxRUqkaXV4ZmJaTks5Zzg Thanks for any input. Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu -- 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] I can't figure out what is wrong with my .gro
On 1/9/13 7:07 PM, Xu Dong Huang wrote: Dear all, I created this .gro file following the gromacs format. But when I load it into VMD, it doesn't show the structure or molecule, and I have made many .gro before this one, and learned from many mistakes, but for this one, I don't know what I did wrong. I still proceeded to do simulation anyway and when I do energy minimization, I get an error of infinite normal force and etc (which I read past gmx list question that an atom is severely overlapping and causing the complication). Since I can't even view the .gro structure i made in VMD, I'm going to go ahead and assume there is something wrong with my initial structure to begin with, but I don't know where. Here is the link to my .gro file + topology https://docs.google.com/open?id=0BwQvutOxRUqkNFMtSmVDanlwRFE https://docs.google.com/open?id=0BwQvutOxRUqkRkNQR2RYS0d6aDA https://docs.google.com/open?id=0BwQvutOxRUqkaXV4ZmJaTks5Zzg The last line of the .gro file (box vectors) does not end in a newline character. I discovered this by running: wc -l star.gro which returned 103, which would indicate that there should be 100 atoms in addition to a title line, number of atoms, and box vectors. Since there are 101 listed atoms, I knew there was a problem, likely with the last line. Adding a newline character allows the structure to be opened in VMD. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] I can't figure out what is wrong with my .gro
@ Justin, Thanks for always saving me from my mistakes. But I don't quite understand what is a new line character? Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 9, 2013, at 7:12 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/9/13 7:07 PM, Xu Dong Huang wrote: Dear all, I created this .gro file following the gromacs format. But when I load it into VMD, it doesn't show the structure or molecule, and I have made many .gro before this one, and learned from many mistakes, but for this one, I don't know what I did wrong. I still proceeded to do simulation anyway and when I do energy minimization, I get an error of infinite normal force and etc (which I read past gmx list question that an atom is severely overlapping and causing the complication). Since I can't even view the .gro structure i made in VMD, I'm going to go ahead and assume there is something wrong with my initial structure to begin with, but I don't know where. Here is the link to my .gro file + topology https://docs.google.com/open?id=0BwQvutOxRUqkNFMtSmVDanlwRFE https://docs.google.com/open?id=0BwQvutOxRUqkRkNQR2RYS0d6aDA https://docs.google.com/open?id=0BwQvutOxRUqkaXV4ZmJaTks5Zzg The last line of the .gro file (box vectors) does not end in a newline character. I discovered this by running: wc -l star.gro which returned 103, which would indicate that there should be 100 atoms in addition to a title line, number of atoms, and box vectors. Since there are 101 listed atoms, I knew there was a problem, likely with the last line. Adding a newline character allows the structure to be opened in VMD. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] I can't figure out what is wrong with my .gro
On 1/9/13 7:16 PM, Xu Dong Huang wrote: @ Justin, Thanks for always saving me from my mistakes. But I don't quite understand what is a new line character? The thing you get when you press enter. http://en.wikipedia.org/wiki/Newline#In_programming_languages Note that Google has plenty more to say ;) There should not be a blank line at the end of the .gro file, though, but to be correctly parsed by VMD, the line must terminate with a '\n' character. So at the end of your box vector line, hit return then backspace. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] I can't figure out what is wrong with my .gro
@ Justin, I laughed. :) Thank you. I can't believe I miss the smallest and most rudimentary things. Thanks again, Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 9, 2013, at 7:20 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/9/13 7:16 PM, Xu Dong Huang wrote: @ Justin, Thanks for always saving me from my mistakes. But I don't quite understand what is a new line character? The thing you get when you press enter. http://en.wikipedia.org/wiki/Newline#In_programming_languages Note that Google has plenty more to say ;) There should not be a blank line at the end of the .gro file, though, but to be correctly parsed by VMD, the line must terminate with a '\n' character. So at the end of your box vector line, hit return then backspace. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] I can't figure out what is wrong with my .gro
@Justin, I did what you suggested, and I still can't load my molecule in VMD. Maybe I am still doing something wrong with the new line character thing. Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 9, 2013, at 7:22 PM, Xu Dong Huang xudo...@eden.rutgers.edu wrote: @ Justin, I laughed. :) Thank you. I can't believe I miss the smallest and most rudimentary things. Thanks again, Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 9, 2013, at 7:20 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/9/13 7:16 PM, Xu Dong Huang wrote: @ Justin, Thanks for always saving me from my mistakes. But I don't quite understand what is a new line character? The thing you get when you press enter. http://en.wikipedia.org/wiki/Newline#In_programming_languages Note that Google has plenty more to say ;) There should not be a blank line at the end of the .gro file, though, but to be correctly parsed by VMD, the line must terminate with a '\n' character. So at the end of your box vector line, hit return then backspace. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] I can't figure out what is wrong with my .gro
On 1/9/13 7:49 PM, Xu Dong Huang wrote: @Justin, I did what you suggested, and I still can't load my molecule in VMD. Maybe I am still doing something wrong with the new line character thing. Go to the last line and go to the end of it. Hit enter. Hit backspace (brings you back up to the vectors line and removes the blank line). Save the file. That's all I did. If you run 'wc -l star.gro' you should get 104 in the terminal instead of 103. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] I can't figure out what is wrong with my .gro
@Justin, I did that, and it still says I have 103. Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 9, 2013, at 7:49 PM, Xu Dong Huang xudo...@eden.rutgers.edu wrote: @Justin, I did what you suggested, and I still can't load my molecule in VMD. Maybe I am still doing something wrong with the new line character thing. Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 9, 2013, at 7:22 PM, Xu Dong Huang xudo...@eden.rutgers.edu wrote: @ Justin, I laughed. :) Thank you. I can't believe I miss the smallest and most rudimentary things. Thanks again, Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 9, 2013, at 7:20 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/9/13 7:16 PM, Xu Dong Huang wrote: @ Justin, Thanks for always saving me from my mistakes. But I don't quite understand what is a new line character? The thing you get when you press enter. http://en.wikipedia.org/wiki/Newline#In_programming_languages Note that Google has plenty more to say ;) There should not be a blank line at the end of the .gro file, though, but to be correctly parsed by VMD, the line must terminate with a '\n' character. So at the end of your box vector line, hit return then backspace. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] I can't figure out what is wrong with my .gro
On 1/9/13 7:58 PM, Xu Dong Huang wrote: @Justin, I did that, and it still says I have 103. I will send you a fixed file off-list so you can compare with what you've got. I don't know what text editor you're using, but I can produce a correct file using two different methods in vi. It's very important to be using a plain text editor when manipulating any Gromacs file. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] I can't figure out what is wrong with my .gro
Oh, you have an Additional line after vector size box…. I thought you said to remove that blank line Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 9, 2013, at 7:58 PM, Xu Dong Huang xudo...@eden.rutgers.edu wrote: @Justin, I did that, and it still says I have 103. Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 9, 2013, at 7:49 PM, Xu Dong Huang xudo...@eden.rutgers.edu wrote: @Justin, I did what you suggested, and I still can't load my molecule in VMD. Maybe I am still doing something wrong with the new line character thing. Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 9, 2013, at 7:22 PM, Xu Dong Huang xudo...@eden.rutgers.edu wrote: @ Justin, I laughed. :) Thank you. I can't believe I miss the smallest and most rudimentary things. Thanks again, Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 9, 2013, at 7:20 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/9/13 7:16 PM, Xu Dong Huang wrote: @ Justin, Thanks for always saving me from my mistakes. But I don't quite understand what is a new line character? The thing you get when you press enter. http://en.wikipedia.org/wiki/Newline#In_programming_languages Note that Google has plenty more to say ;) There should not be a blank line at the end of the .gro file, though, but to be correctly parsed by VMD, the line must terminate with a '\n' character. So at the end of your box vector line, hit return then backspace. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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] I can't figure out what is wrong with my .gro
On 1/9/13 8:02 PM, Xu Dong Huang wrote: Oh, you have an Additional line after vector size box…. I thought you said to remove that blank line There is no additional line. The last line in the file must be the box vectors. -Justin Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 9, 2013, at 7:58 PM, Xu Dong Huang xudo...@eden.rutgers.edu wrote: @Justin, I did that, and it still says I have 103. Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 9, 2013, at 7:49 PM, Xu Dong Huang xudo...@eden.rutgers.edu wrote: @Justin, I did what you suggested, and I still can't load my molecule in VMD. Maybe I am still doing something wrong with the new line character thing. Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 9, 2013, at 7:22 PM, Xu Dong Huang xudo...@eden.rutgers.edu wrote: @ Justin, I laughed. :) Thank you. I can't believe I miss the smallest and most rudimentary things. Thanks again, Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 9, 2013, at 7:20 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/9/13 7:16 PM, Xu Dong Huang wrote: @ Justin, Thanks for always saving me from my mistakes. But I don't quite understand what is a new line character? The thing you get when you press enter. http://en.wikipedia.org/wiki/Newline#In_programming_languages Note that Google has plenty more to say ;) There should not be a blank line at the end of the .gro file, though, but to be correctly parsed by VMD, the line must terminate with a '\n' character. So at the end of your box vector line, hit return then backspace. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] I can't figure out what is wrong with my .gro
Must be something wrong with my editor program (BBEdit), because when I open the file you sent me, it shows me there an additional blank line. Ok, time to switch to regular text editor… Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 9, 2013, at 8:04 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/9/13 8:02 PM, Xu Dong Huang wrote: Oh, you have an Additional line after vector size box…. I thought you said to remove that blank line There is no additional line. The last line in the file must be the box vectors. -Justin Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 9, 2013, at 7:58 PM, Xu Dong Huang xudo...@eden.rutgers.edu wrote: @Justin, I did that, and it still says I have 103. Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 9, 2013, at 7:49 PM, Xu Dong Huang xudo...@eden.rutgers.edu wrote: @Justin, I did what you suggested, and I still can't load my molecule in VMD. Maybe I am still doing something wrong with the new line character thing. Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 9, 2013, at 7:22 PM, Xu Dong Huang xudo...@eden.rutgers.edu wrote: @ Justin, I laughed. :) Thank you. I can't believe I miss the smallest and most rudimentary things. Thanks again, Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 9, 2013, at 7:20 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/9/13 7:16 PM, Xu Dong Huang wrote: @ Justin, Thanks for always saving me from my mistakes. But I don't quite understand what is a new line character? The thing you get when you press enter. http://en.wikipedia.org/wiki/Newline#In_programming_languages Note that Google has plenty more to say ;) There should not be a blank line at the end of the .gro file, though, but to be correctly parsed by VMD, the line must terminate with a '\n' character. So at the end of your box vector line, hit return then backspace. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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
[gmx-users] EM error
Dear users, Now I fixed the initial structure error, and I solvated it in water (martini bead model), and i run typical EM, I get the following error: Steepest Descents: Tolerance (Fmax) = 1.0e+01 Number of steps=5 Step= 14, Dmax= 1.2e-06 nm, Epot= 4.48322e+19 Fmax= inf, atom= 14524 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 10 Double precision normally gives you higher accuracy. writing lowest energy coordinates. Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 10. Potential Energy = 4.4832208e+19 Maximum force =inf on atom 14524 Norm of force =inf gcq#182: That Was Cool (Beavis and Butthead) -My EM.mdp file contains the following: integrator = steep dt = 0.020 nsteps = 5 ;Note: 100 steps is to much for a vacuum run (nsteps=10) nstlog = 1000 nstenergy= 500 nstxtcout= 500 nstlist = 10 ns_type = grid pbc = xyz periodic_molecules = no rlist= 1.4 coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 epsilon_r= 15 epsilon_rf = 1 vdw_type = Shift rvdw_switch = 0.9 rvdw = 1.2 My system size 73191 W, and 1 star (consisted of 101 atoms) I read somewhere that it's that atom 14524 is overlapping… I can't visually see anything complicated in my VMD since the system is pretty big Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu -- 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] EM error
Everytime I remove the atom that is causing the INF force, it gives me new atom that causes INF force. (The ones that come up are all water beads that are causing the infinite force), does that mean when i did genbox it inserted water incorrectly? (Because I viewed it in VMD it's certainly not overlapping with my solute. ) Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 9, 2013, at 8:12 PM, Xu Dong Huang xudo...@eden.rutgers.edu wrote: Dear users, Now I fixed the initial structure error, and I solvated it in water (martini bead model), and i run typical EM, I get the following error: Steepest Descents: Tolerance (Fmax) = 1.0e+01 Number of steps=5 Step= 14, Dmax= 1.2e-06 nm, Epot= 4.48322e+19 Fmax= inf, atom= 14524 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 10 Double precision normally gives you higher accuracy. writing lowest energy coordinates. Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 10. Potential Energy = 4.4832208e+19 Maximum force =inf on atom 14524 Norm of force =inf gcq#182: That Was Cool (Beavis and Butthead) -My EM.mdp file contains the following: integrator = steep dt = 0.020 nsteps = 5 ;Note: 100 steps is to much for a vacuum run (nsteps=10) nstlog = 1000 nstenergy= 500 nstxtcout= 500 nstlist = 10 ns_type = grid pbc = xyz periodic_molecules = no rlist= 1.4 coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 epsilon_r= 15 epsilon_rf = 1 vdw_type = Shift rvdw_switch = 0.9 rvdw = 1.2 My system size 73191 W, and 1 star (consisted of 101 atoms) I read somewhere that it's that atom 14524 is overlapping… I can't visually see anything complicated in my VMD since the system is pretty big Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu -- 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] EM error
On 1/9/13 8:42 PM, Xu Dong Huang wrote: Everytime I remove the atom that is causing the INF force, it gives me new atom that causes INF force. (The ones that come up are all water beads that are causing the infinite force), does that mean when i did genbox it inserted water incorrectly? (Because I viewed it in VMD it's certainly not overlapping with my solute. ) It seems like all the waters are being placed too close to the polymer beads, so you should probably increase the value of -vdwd when running genbox. You can make your life easier in visualization by selecting only certain atoms to display, i.e. by using the Tk console: set myatoms [atomselect 0 (within 5 of index 14523)] animate write pdb myfile.pdb sel $myatoms That saves the coordinates of any atom within 5 Angstrom of the problematic atom below (14524, or index 14523). Displaying these atoms only can be much more useful than trying to sift through 7+ atoms. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] EM error
@ Justin, Thank you, that worked like a charm! (Using increased vanderwal distance) Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 9, 2013, at 8:42 PM, Xu Dong Huang xudo...@eden.rutgers.edu wrote: Everytime I remove the atom that is causing the INF force, it gives me new atom that causes INF force. (The ones that come up are all water beads that are causing the infinite force), does that mean when i did genbox it inserted water incorrectly? (Because I viewed it in VMD it's certainly not overlapping with my solute. ) Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 9, 2013, at 8:12 PM, Xu Dong Huang xudo...@eden.rutgers.edu wrote: Dear users, Now I fixed the initial structure error, and I solvated it in water (martini bead model), and i run typical EM, I get the following error: Steepest Descents: Tolerance (Fmax) = 1.0e+01 Number of steps=5 Step= 14, Dmax= 1.2e-06 nm, Epot= 4.48322e+19 Fmax= inf, atom= 14524 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 10 Double precision normally gives you higher accuracy. writing lowest energy coordinates. Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 10. Potential Energy = 4.4832208e+19 Maximum force =inf on atom 14524 Norm of force =inf gcq#182: That Was Cool (Beavis and Butthead) -My EM.mdp file contains the following: integrator = steep dt = 0.020 nsteps = 5 ;Note: 100 steps is to much for a vacuum run (nsteps=10) nstlog = 1000 nstenergy= 500 nstxtcout= 500 nstlist = 10 ns_type = grid pbc = xyz periodic_molecules = no rlist= 1.4 coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 epsilon_r= 15 epsilon_rf = 1 vdw_type = Shift rvdw_switch = 0.9 rvdw = 1.2 My system size 73191 W, and 1 star (consisted of 101 atoms) I read somewhere that it's that atom 14524 is overlapping… I can't visually see anything complicated in my VMD since the system is pretty big Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] gromacs on GPU
Hi James, The build looks mostly fine except that you are using fftw3 compiled with AVX which is slower than with only SSE (even on AVX-capable CPUs) - you should have been warned about this at configure-time. Now, performance-wise everything looks fine except that with a 1.2 nm cut-off your GPU is not able to keep up with the CPU and finish the non-bonded work before the CPU is done with Bonded + PME. That's why you see the Wait GPU taking 20% of the total time and that's also why you see some cores idling (because for 20% of the run-time thread 0 on core 0 is blocked waiting for the GPU while the rest idle). As the suggestion at the end of the log file point out, you can consider using a shorter cut-off which will push more work back to the PME on the CPU, but whether you can do this it depends on your very problem. There is one more alternative of running two MPI processes on the GPU (mpirun -np 2 mdrun -gpu_id 00) and using the -nb gpu_cpu mode which will execute part of the nonbonded on the CPU, but this might not help. Cheers, -- Szilárd On Wed, Jan 9, 2013 at 8:27 PM, James Starlight jmsstarli...@gmail.comwrote: Dear Szilárd, thanks for help again! 2013/1/9 Szilárd Páll szilard.p...@cbr.su.se: There could be, but I/we can't well without more information on what and how you compiled and ran. The minimum we need is a log file. I've compilated gromacs 4.6-3 beta via simple cmake CMakeLists.txt -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-5.0 make sudo make install I have not added any special params to the grompp or mdrun. After that I've run tested simulation of the calmodulin in explicit water ( 60k atoms ) 100ps and obtain next output Host: starlight pid: 21028 nodeid: 0 nnodes: 1 Gromacs version:VERSION 4.6-beta3 Precision: single MPI library:thread_mpi OpenMP support: enabled GPU support:enabled invsqrt routine:gmx_software_invsqrt(x) CPU acceleration: AVX_256 FFT library:fftw-3.3.2-sse2-avx Large file support: enabled RDTSCP usage: enabled Built on: Wed Jan 9 20:44:51 MSK 2013 Built by: own@starlight [CMAKE] Build OS/arch: Linux 3.2.0-2-amd64 x86_64 Build CPU vendor: GenuineIntel Build CPU brand:Intel(R) Core(TM) i5-3570 CPU @ 3.40GHz Build CPU family: 6 Model: 58 Stepping: 9 Build CPU features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic C compiler: /usr/bin/gcc GNU gcc (Debian 4.6.3-11) 4.6.3 C compiler flags: -mavx -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG C++ compiler: /usr/bin/c++ GNU c++ (Debian 4.6.3-11) 4.6.3 C++ compiler flags: -mavx -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG CUDA compiler: nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2012 NVIDIA Corporation;Built on Fri_Sep_21_17:28:58_PDT_2012;Cuda compilation tools, release 5.0, V0.2.1221 CUDA driver:5.0 CUDA runtime: 5.0 Core t (s) Wall t (s)(%) Time: 2770.700 1051.927 263.4 (ns/day)(hour/ns) Performance:8.2142.922 full log can be found here http://www.sendspace.com/file/inum84 Finally when I check CPU usage I notice that only 1 CPU was full loaded ( 100%) and 2-4 cores were loaded on only 60% but gave me strange results that GPU is not used (I've only monitored temperature of video card and noticed increase of the temperature up to 65 degrees ) +--+ | NVIDIA-SMI 4.304.54 Driver Version: 304.54 | |---+--+--+ | GPU Name | Bus-IdDisp. | Volatile Uncorr. ECC | | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. | |===+==+==| | 0 GeForce GTX 670 | :02:00.0 N/A | N/A | | 38% 63C N/A N/A / N/A | 9% 174MB / 2047MB | N/A Default | +---+--+--+ +-+ | Compute processes: GPU Memory | | GPU PID Process name Usage | |=| |0Not Supported | +-+
[gmx-users] Re: gmx-users Digest, Vol 105, Issue 43
thank you Justin.Now it is fine. -- Message: 1 Date: Wed, 9 Jan 2013 22:50:13 +0530 From: SANTU BISWAS santu.biswa...@gmail.com Subject: [gmx-users] energy-mimisation-problem To: gmx-users@gromacs.org Message-ID: caewz1z-7yv_8dcaurt+rm6fkdqomcmftxpdkbzl0atyyoor...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 dear users, I am performing an energy minimization of apolypeptide(formed by alanine-10-residues) in vacuum box by using Steepest Descent(initially) and then Conjugate Gradient methods in gromacs_4.5.5_doubleprecision.The chain length of alanine-10-mer is around 1.5 nm.Here i want to see only the sort-range interactions.so i use cutoff 2.0 nm .But in the output (.log )file there is a contribution of energy for long-range interactions(in both energy minimisation methods). I do not understand why this is happening. the input file for energy minimisation is, ;title= cpp = /lib/cpp ;include =-I../top/ define = -DFLEXIBLE ; Input file integrator = steep/cg nsteps = 1 nstlist = 1 rlist = 1.0 rcoulomb= 2.0 rvdw= 2.0 ; Energy minimizing stuff emtol = 0.001 emstep = 0.1 nstcgsteep = 10 the output(.log )file is, Energies (kJ/mol) Bond AngleProper Dih. Ryckaert-Bell. LJ-14 8.48244e+002.10205e+012.39409e+00 9.86941e+01 1.47894e+02 Coulomb-14LJ (SR)LJ (LR) Coulomb (SR) Coulomb (LR) 1.63221e+03 -1.64038e+02 -4.97232e-01 -3.00455e+03 -1.00138e+01 Potential Pressure (bar) -1.26841e+030.0e+00 santu -- Message: 2 Date: Wed, 09 Jan 2013 12:30:06 -0500 From: Justin Lemkul jalem...@vt.edu Subject: Re: [gmx-users] energy-mimisation-problem To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 50eda91e.2070...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 1/9/13 12:20 PM, SANTU BISWAS wrote: dear users, I am performing an energy minimization of apolypeptide(formed by alanine-10-residues) in vacuum box by using Steepest Descent(initially) and then Conjugate Gradient methods in gromacs_4.5.5_doubleprecision.The chain length of alanine-10-mer is around 1.5 nm.Here i want to see only the sort-range interactions.so i use cutoff 2.0 nm .But in the output (.log )file there is a contribution of energy for long-range interactions(in both energy minimisation methods). I do not understand why this is happening. the input file for energy minimisation is, ;title= cpp = /lib/cpp ;include =-I../top/ define = -DFLEXIBLE ; Input file integrator = steep/cg nsteps = 1 nstlist = 1 rlist = 1.0 rcoulomb= 2.0 rvdw= 2.0 ; Energy minimizing stuff emtol = 0.001 emstep = 0.1 nstcgsteep = 10 You haven't set a value for the pbc keyword, so it takes the default value (xyz). The result is that you're not really minimizing in vacuo, but rather in some sort of pseudo-crystal state that probably has lots of periodicity artifacts. That's probably the source of the energy terms - your peptide interacting with itself. -Justin the output(.log )file is, Energies (kJ/mol) Bond AngleProper Dih. Ryckaert-Bell. LJ-14 8.48244e+002.10205e+012.39409e+00 9.86941e+01 1.47894e+02 Coulomb-14LJ (SR)LJ (LR) Coulomb (SR) Coulomb (LR) 1.63221e+03 -1.64038e+02 -4.97232e-01 -3.00455e+03 -1.00138e+01 Potential Pressure (bar) -1.26841e+030.0e+00 santu -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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: .HTP FILE
Hi Boopathi, Adding hydrogen atoms to the hdb is explained in the sectio 5.6.4 of gromacs manual 4.5.4. Please refer the manual. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Thu, Jan 10, 2013 at 11:32 AM, Subramaniam Boopathi boopathi...@gmail.com wrote: Dear All I have created the pdb file for interaction of protein with new molecules. I am able to rum the pdb file successfully but I am facing error in the Equillibration process. The Error shows that *atom HAQ is missing in residue NIC 8 in the pdb file You might need to add atom HAQ to the hydrogen database of building block NIC in the file aminoacids.hdb (see the manual) * likewise 14 atoms H atoms are missing in residu*e.Can anyone help me how to add atom in .htp file for new molecules interacting with protein.Thanks in advance. with regards Boopathi.s * -- 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 on GPU
Szilárd , thanks again for explanation! Today I've performed some tests on my calmodulin in water system with different cutt-offs (I've used all cutt-ooffs 1.0 , 0.9 and 0.8 respectually) Below you can see that the highest performance was in case of 0.8 cut-offs all cut-offs 1.0 Force evaluation time GPU/CPU: 6.134 ms/4.700 ms = 1.305 NOTE: The GPU has 20% more load than the CPU. This imbalance causes performance loss, consider using a shorter cut-off and a finer PME grid. Core t (s) Wall t (s)(%) Time: 1313.420 464.035 283.0 (ns/day)(hour/ns) Performance:9.3102.578 Finished mdrun on node 0 Thu Jan 10 09:39:23 2013 all cut-offs 0.9 Force evaluation time GPU/CPU: 4.951 ms/4.675 ms = 1.059 Core t (s) Wall t (s)(%) Time: 2414.930 856.179 282.1 (ns/day)(hour/ns) Performance: 10.0922.378 Finished mdrun on node 0 Thu Jan 10 10:09:52 2013 all cut-offs 0.8 Force evaluation time GPU/CPU: 4.001 ms/4.659 ms = 0.859 Core t (s) Wall t (s)(%) Time: 1166.390 413.598 282.0 (ns/day)(hour/ns) Performance: 10.4452.298 Finished mdrun on node 0 Thu Jan 10 09:50:33 2013 Also I've noticed that 2-4 CPU cores usage in 2 and 3rd case was only 67%. Is there any other ways to increase performance by means of neighboor search parameters ( e.g nstlist etc) ? Might such reduced cut-off be used with the force fields ( e,g charmm) where initially usage of longest cut-offs have given better results (e,g in charmm27 and gromos56 I always use 1.2 and 1.4 nm for rvdw, respectually) ? James 2013/1/10 Szilárd Páll szilard.p...@cbr.su.se: Hi James, The build looks mostly fine except that you are using fftw3 compiled with AVX which is slower than with only SSE (even on AVX-capable CPUs) - you should have been warned about this at configure-time. Now, performance-wise everything looks fine except that with a 1.2 nm cut-off your GPU is not able to keep up with the CPU and finish the non-bonded work before the CPU is done with Bonded + PME. That's why you see the Wait GPU taking 20% of the total time and that's also why you see some cores idling (because for 20% of the run-time thread 0 on core 0 is blocked waiting for the GPU while the rest idle). As the suggestion at the end of the log file point out, you can consider using a shorter cut-off which will push more work back to the PME on the CPU, but whether you can do this it depends on your very problem. There is one more alternative of running two MPI processes on the GPU (mpirun -np 2 mdrun -gpu_id 00) and using the -nb gpu_cpu mode which will execute part of the nonbonded on the CPU, but this might not help. Cheers, -- Szilárd On Wed, Jan 9, 2013 at 8:27 PM, James Starlight jmsstarli...@gmail.comwrote: Dear Szilárd, thanks for help again! 2013/1/9 Szilárd Páll szilard.p...@cbr.su.se: There could be, but I/we can't well without more information on what and how you compiled and ran. The minimum we need is a log file. I've compilated gromacs 4.6-3 beta via simple cmake CMakeLists.txt -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-5.0 make sudo make install I have not added any special params to the grompp or mdrun. After that I've run tested simulation of the calmodulin in explicit water ( 60k atoms ) 100ps and obtain next output Host: starlight pid: 21028 nodeid: 0 nnodes: 1 Gromacs version:VERSION 4.6-beta3 Precision: single MPI library:thread_mpi OpenMP support: enabled GPU support:enabled invsqrt routine:gmx_software_invsqrt(x) CPU acceleration: AVX_256 FFT library:fftw-3.3.2-sse2-avx Large file support: enabled RDTSCP usage: enabled Built on: Wed Jan 9 20:44:51 MSK 2013 Built by: own@starlight [CMAKE] Build OS/arch: Linux 3.2.0-2-amd64 x86_64 Build CPU vendor: GenuineIntel Build CPU brand:Intel(R) Core(TM) i5-3570 CPU @ 3.40GHz Build CPU family: 6 Model: 58 Stepping: 9 Build CPU features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic C compiler: /usr/bin/gcc GNU gcc (Debian 4.6.3-11) 4.6.3 C compiler flags: -mavx -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG C++ compiler: /usr/bin/c++ GNU c++ (Debian 4.6.3-11) 4.6.3 C++ compiler flags: -mavx -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG CUDA compiler: nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2012 NVIDIA
[gmx-users] necessity of energy minimization
Hi All, when I run energy minimization the system gives error, and broke up. it has error about steep integrator and says tha: steepest time is too small. but the system is running by MD integrator without any em step). is the energy minimization necessary to all cases? for example in DL_POL software we dont have enegy minimization , seperately. is it correct that I start simulation steps by md integrator and NVT ensemble? tnx Niki -- 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
