Re: [gmx-users] GPU job failed
Hi, from the double output it looks like two identical mdruns, each with 1 PP process and 10 OpenMP threads, are started. Maybe there is something wrong with your MPI setup (did you by mistake compile with thread-MPI instead of MPI?) Carsten On 09 Sep 2014, at 09:06, Albert mailmd2...@gmail.com wrote: Here are more informations from log file: mpirun -np 2 mdrun_mpi -v -s npt2.tpr -c npt2.gro -x npt2.xtc -g npt2.log -gpu_id 01 -ntomp 0 Number of hardware threads detected (20) does not match the number reported by OpenMP (10). Consider setting the launch configuration manually! Number of hardware threads detected (20) does not match the number reported by OpenMP (10). Consider setting the launch configuration manually! Reading file npt2.tpr, VERSION 5.0.1 (single precision) Reading file npt2.tpr, VERSION 5.0.1 (single precision) Using 1 MPI process Using 10 OpenMP threads 2 GPUs detected on host cudaB: #0: NVIDIA GeForce GTX 780 Ti, compute cap.: 3.5, ECC: no, stat: compatible #1: NVIDIA GeForce GTX 780 Ti, compute cap.: 3.5, ECC: no, stat: compatible 2 GPUs user-selected for this run. Mapping of GPUs to the 1 PP rank in this node: #0, #1 --- Program mdrun_mpi, VERSION 5.0.1 Source code file: /soft2/plumed-2.2/gromacs-5.0.1/src/gromacs/gmxlib/gmx_detect_hardware.c, line: 359 Fatal error: Incorrect launch configuration: mismatching number of PP MPI processes and GPUs per node. mdrun_mpi was started with 1 PP MPI process per node, but you provided 2 GPUs. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Halting program mdrun_mpi gcq#314: Do You Have Sex Maniacs or Schizophrenics or Astrophysicists in Your Family? (Gogol Bordello) -- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode -1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -- Using 1 MPI process Using 10 OpenMP threads 2 GPUs detected on host cudaB: #0: NVIDIA GeForce GTX 780 Ti, compute cap.: 3.5, ECC: no, stat: compatible #1: NVIDIA GeForce GTX 780 Ti, compute cap.: 3.5, ECC: no, stat: compatible 2 GPUs user-selected for this run. Mapping of GPUs to the 1 PP rank in this node: #0, #1 --- Program mdrun_mpi, VERSION 5.0.1 Source code file: /soft2/plumed-2.2/gromacs-5.0.1/src/gromacs/gmxlib/gmx_detect_hardware.c, line: 359 Fatal error: Incorrect launch configuration: mismatching number of PP MPI processes and GPUs per node. mdrun_mpi was started with 1 PP MPI process per node, but you provided 2 GPUs. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Halting program mdrun_mpi gcq#56: Lunatics On Pogo Sticks (Red Hot Chili Peppers) -- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode -1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -- On 09/08/2014 11:59 PM, Yunlong Liu wrote: Same idea with Szilard. How many nodes are you using? On one nodes, how many MPI ranks do you have? The error is complaining about you assigned two GPUs to only one MPI process on one node. If you spread your two MPI ranks on two nodes, that means you only have one at each. Then you can't assign two GPU for only one MPI rank. How many GPU do you have on one node? If there are two, you can either launch two PPMPI processes on one node and assign two GPU for them. If you only want to launch one MPI rank on each node, you can assign only one GPU for each node ( by -gpu_id 0 ) Yunlong -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302
Re: [gmx-users] GPU job failed
thank you for reply. I compiled it with command: env CC=mpicc CXX=mpicxx F77=mpif90 FC=mpif90 LDF90=mpif90 CMAKE_PREFIX_PATH=/home/albert/install/intel-2013/mkl/include/fftw:/home/albert/install/intel-mpi/bin64 cmake .. -DBUILD_SHARED_LIB=OFF -DBUILD_TESTING=OFF -DCMAKE_INSTALL_PREFIX=/home/albert/install/gromacs-5.0.1_plumed_2.2-intel -DGMX_MPI=ON -DGMX_GPU=ON -DGMX_PREFER_STATIC_LIBS=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-6.0 On 09/09/2014 09:16 AM, Carsten Kutzner wrote: Hi, from the double output it looks like two identical mdruns, each with 1 PP process and 10 OpenMP threads, are started. Maybe there is something wrong with your MPI setup (did you by mistake compile with thread-MPI instead of MPI?) Carsten -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] GPU job failed
thank you for reply. I compiled it with command: env CC=mpicc CXX=mpicxx F77=mpif90 FC=mpif90 LDF90=mpif90 CMAKE_PREFIX_PATH=/home/albert/install/intel-2013/mkl/include/fftw:/home/albert/install/intel-mpi/bin64 cmake .. -DBUILD_SHARED_LIB=OFF -DBUILD_TESTING=OFF -DCMAKE_INSTALL_PREFIX=/home/albert/install/gromacs-5.0.1_plumed_2.2-intel -DGMX_MPI=ON -DGMX_GPU=ON -DGMX_PREFER_STATIC_LIBS=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-6.0 On 09/09/2014 09:16 AM, Carsten Kutzner wrote: Hi, from the double output it looks like two identical mdruns, each with 1 PP process and 10 OpenMP threads, are started. Maybe there is something wrong with your MPI setup (did you by mistake compile with thread-MPI instead of MPI?) Carsten -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] GPU job failed
I recompiled Gromacs-5.0.1, finally it works now Probably I made some mistakes in previous compiling thanks a lot guys regards Albert On 09/09/2014 09:16 AM, Carsten Kutzner wrote: Hi, from the double output it looks like two identical mdruns, each with 1 PP process and 10 OpenMP threads, are started. Maybe there is something wrong with your MPI setup (did you by mistake compile with thread-MPI instead of MPI?) Carsten -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] PBC only on x and y in an NPT ensemble
Dear all I would like to simulate coarse grained thin polymer films supported on a wall or a substrate (I don't really mind) but with the one interface to be free. I would like to do this under NPT conditions. I would expect that this can only be done by putting pbc=xy, as in the to the following study: http://pubs.acs.org/doi/abs/10.1021/ma102567s but this option is not supported in GROMACS without the usage of walls. Is there any other way to simulated supported films in GROMACS under NPT conditions? Thanks in advance, Tommy -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Spherical Position Restrain from the center of the Box
Dear gromacs user: I plan to do a coarse grain simulation for a whole virus coat. It only contains virus surface protein, so I'm afraid it will collapse due to lack of inner member lipids. I plan to add a Spherical Position Restrain from the center of the Box, to prevent the surface protein fall inside of the sphere, but allow the surface protein move outward. Can anyone tell me how to make such a position restrain in gromacs? Thanks a lot. Best regards, Haiping Zhang -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Query regarding the addition of solvent molecule
On 9/9/14 12:51 AM, Christina Florina wrote: Hi, I have included the link to my dropbox where I have attached my gromacs topology files. Though I have included the cyclohexane itp file in the .top file still I am the same error NO SUCH MOLECULETYPE CHX. SO, Kindly need help in this regard. Thank you in advance. https://www.dropbox.com/sh/vkvsr3u2hmh2ft9/AABxNv6VxA1gbSs7h2gkaIfxa?dl=0 You have several problems: 1. The #include statement for chx.itp is probably wrong (though I don't know how you're organizing your files), but unless you've put chx.itp in the force field directory, #include gromos43a1.ff/chx.itp is incorrect. 2. The contents of chx.itp are wrong for several reasons. The #ifndef lines are nonsensical and need to be deleted. The #include statement for water needs to be deleted. The [system] and [molecules] levels (which are system-level and thus can only go in a .top) need to be deleted. -Justin On Fri, Sep 5, 2014 at 5:25 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/5/14, 7:10 AM, Christina Florina wrote: Hi, I have included the chx.itp file in the protein.top file already. Checked with the molecule name (CHX) in the .itp file and also in the topology file variable name which matches CHX. But still I am getting the same error. Kindly need help to resolve it. Something doesn't add up. You will need to provide all of your files for download via a file-sharing service to diagnose. A simple #include statement and correct updating of [molecules] is all that is needed. -Justin On Fri, Sep 5, 2014 at 3:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/5/14, 2:50 AM, Christina Florina wrote: Hi, I have just started my work in MD and using Gromacs 5.0. I need to use cyclohexane as my solvent instead of water. I generated the topology file, .itp and .gro using PRODRG. I have successfully incorporated the .gro file using solvate command and generated the solvent box. But I am facing problem with grompp (ions.mdp) step before the addition of ions. gmx grompp -f ions.mdp -c protein_solv.gro -p protein.top -o ions.tpr I am getting the FATAL ERROR: NO SUCH MOLECULETYPE CHX though I have checked with the molecule name (CHX) in the cyclohexane .itp file. I have tired changing the name of the molecule also. Do I need to add this cyclohexane solvent molecule in the forcefield file or .atp file, .rtp file? I tried adding them but still not able to run this. I might be incorrect while adding it in the .rtp file. So, I kindly need help regarding the addition of new solvent molecule in gromacs since I have other organic solvents also for my md work and having the same problem. You need to #include the CHX .itp file in the system .top, and update [molecules] accordingly. Please note as well that PRODRG topologies are of low quality in my experience and need to be corrected. CHX is simple, a ring of CH2 atom types, all with zero charge. Other results are less trivial to fix. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441
[gmx-users] Postdoc Position Available
A postdoctoral position in computational physics of Carbon Nano Tubes (CNTs) is available at Khalifa University, Abu Dhabi, UAE.The successful candidate will work in a highly collaborative environment with experimental and theoretical scientist. The candidate should have a good knowledge of Molecular Dynamics simulations and statistical mechanics. Candidates with background in physics, physical chemistry, biophysics and engineering are desirable. Candidates also should have experience with large-scale computing.For further information please contact Dirar Al Homouz at dirar_at_hotmail.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Query regarding the addition of solvent molecule
Hi, Thanks for your suggestions. If the .itp file has error, is there any other way to generate .itp files for the solvents or do i need to write them manually? Because the .itp files I have attached are generated using PRODRG. If I edit the chx.itp file based on the corrections you have told, will it be fine? I am getting the same error for all the 4 solvent files I have generated using PRODRG. I do not get the .itp and .gro files online or tutorials for the organic solvents i am using for my md studies. I have included the .itp file in both top directory and force field directory. It might be the reason the .gro file could be read in the solvate step. But how to make it in a correct format to proceed with? I am new to gromacs using other organic solvents apart from water and default solvents in gromacs package. So, kindly need help how to build an .itp file and .gro file for a solvent and to resolve the issue. On Tue, Sep 9, 2014 at 3:38 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/9/14 12:51 AM, Christina Florina wrote: Hi, I have included the link to my dropbox where I have attached my gromacs topology files. Though I have included the cyclohexane itp file in the .top file still I am the same error NO SUCH MOLECULETYPE CHX. SO, Kindly need help in this regard. Thank you in advance. https://www.dropbox.com/sh/vkvsr3u2hmh2ft9/AABxNv6VxA1gbSs7h2gkaIfxa?dl=0 You have several problems: 1. The #include statement for chx.itp is probably wrong (though I don't know how you're organizing your files), but unless you've put chx.itp in the force field directory, #include gromos43a1.ff/chx.itp is incorrect. 2. The contents of chx.itp are wrong for several reasons. The #ifndef lines are nonsensical and need to be deleted. The #include statement for water needs to be deleted. The [system] and [molecules] levels (which are system-level and thus can only go in a .top) need to be deleted. -Justin On Fri, Sep 5, 2014 at 5:25 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/5/14, 7:10 AM, Christina Florina wrote: Hi, I have included the chx.itp file in the protein.top file already. Checked with the molecule name (CHX) in the .itp file and also in the topology file variable name which matches CHX. But still I am getting the same error. Kindly need help to resolve it. Something doesn't add up. You will need to provide all of your files for download via a file-sharing service to diagnose. A simple #include statement and correct updating of [molecules] is all that is needed. -Justin On Fri, Sep 5, 2014 at 3:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/5/14, 2:50 AM, Christina Florina wrote: Hi, I have just started my work in MD and using Gromacs 5.0. I need to use cyclohexane as my solvent instead of water. I generated the topology file, .itp and .gro using PRODRG. I have successfully incorporated the .gro file using solvate command and generated the solvent box. But I am facing problem with grompp (ions.mdp) step before the addition of ions. gmx grompp -f ions.mdp -c protein_solv.gro -p protein.top -o ions.tpr I am getting the FATAL ERROR: NO SUCH MOLECULETYPE CHX though I have checked with the molecule name (CHX) in the cyclohexane .itp file. I have tired changing the name of the molecule also. Do I need to add this cyclohexane solvent molecule in the forcefield file or .atp file, .rtp file? I tried adding them but still not able to run this. I might be incorrect while adding it in the .rtp file. So, I kindly need help regarding the addition of new solvent molecule in gromacs since I have other organic solvents also for my md work and having the same problem. You need to #include the CHX .itp file in the system .top, and update [molecules] accordingly. Please note as well that PRODRG topologies are of low quality in my experience and need to be corrected. CHX is simple, a ring of CH2 atom types, all with zero charge. Other results are less trivial to fix. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. --
[gmx-users] Modifying the protein chain in GROMACS
Dear all, I am currently trying to “mutate a protein by changing its backbone directly, i.e. I am not interested in changing a specific amino acid against another (I’ve found out that you can use VMD or Pymol for this purpose), but I am rather interested in changing certain atoms in the backbone by another functional group. In other words, I would like to replace, e.g., the NH-C=O-CR unit of a certain amino acid by a couple of other atoms which do not comprise a peptide bond (e.g. a small aromatic ring). After this, I would like to run MD simulations. How would I do this? Is this actually possible? I would really appreciate your help, because I have no idea how to do the first steps of setting up the calculation (generating an input file that pdb2gmx can read, etc.). Neither an extensive Google search nor the GROMACS manual were useful to me in this respect. Best wishes, Tim -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Modifying the protein chain in GROMACS
On 9/9/14 8:51 AM, Tim Stauch wrote: Dear all, I am currently trying to “mutate a protein by changing its backbone directly, i.e. I am not interested in changing a specific amino acid against another (I’ve found out that you can use VMD or Pymol for this purpose), but I am rather interested in changing certain atoms in the backbone by another functional group. In other words, I would like to replace, e.g., the NH-C=O-CR unit of a certain amino acid by a couple of other atoms which do not comprise a peptide bond (e.g. a small aromatic ring). After this, I would like to run MD simulations. How would I do this? Is this actually possible? I would really appreciate your help, because I have no idea how to do the first steps of setting up the calculation (generating an input file that pdb2gmx can read, etc.). Neither an extensive Google search nor the GROMACS manual were useful to me in this respect. The solution is here: http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field The key issues are (1) generating the .rtp entry, (2) deriving suitable parameters for whatever the residue(s) is(are), and (3) building a coordinate file for pdb2gmx to read. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] mean square displacement
Hello all I would like to plot mean square displacement of hydrogen atoms of protein versus temperature (in order to get dynamical transition temperature). I am using g_msd for this purpose (g_msd -f *_nopbc.xtc -s *.tpr -n index.ndx -o *.xvg) . I am getting following curves as uploded in : http://s903.photobucket.com/user/nidhikatyal1989/media/msd_fig1_zpsc293a5ab.jpg.html How should I plot msd value versus temperature? Is it reasonable enough to take average over 2 ns (linear part) and discard the rest? Moreover, I suspect there is something wrong in the curves too since they are increasing first, reaching saturation and again increasing (last part is unexpected). Actually I am trying to reproduce the results of following paper: THE JOURNAL OF CHEMICAL PHYSICS 130, 135101 2009, FIG 9 (a) My values are also deviating by larger amount. Am I doing something wrong? Please help. Thanks Nidhi -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Gromacs 5.0 compilation slower than 4.6.5. What wentwrong ?
Thank you very much to all of you. That should explain the difference in performance. I'll also discuss it with a more gromacs-knowledgeable colleague of mine. Best Regards. 2014-09-06 8:58 GMT+02:00 Abhi Acharya abhi117acha...@gmail.com: Thank you Mark and Szilard for your replies. It gave more clarity on how the new gromacs works, especially in greater support for streamed computing. I hope David's problem is sorted too. :) Thanks again, Regards, Abhishek Acharya On Fri, Sep 5, 2014 at 10:45 PM, Szilárd Páll pall.szil...@gmail.com wrote: On Fri, Sep 5, 2014 at 6:40 PM, Abhishek Acharya abhi117acha...@gmail.com wrote: Dear Mark, Thank you for the insightful reply. In the manual for gromacs 5.0 it was mentioned that verlet scheme is better for GPU systems. More correctly, only the Verlet scheme supports GPU acceleration. The algorithms used by the group scheme are not appropriate for GPUs or other wide-SIMD accelerators. Does that mean that we should give up on the group scheme scheme, even though we get good performance compared to verlet? That's up to you to decide. The algorithms are different, the group scheme does not use a buffer by default, while the verlet scheme does and aims to control the drift (and keep it quite low by default). Future plan of removing group cut-off scheme indicates that it must have been associated with a high cost-benefit ratio. What makes you conclude that? The reasons are described here: http://www.gromacs.org/Documentation/Cut-off_schemes In very brief summary: i) the groups scheme is not suitable for accelerators and wide SIMD architectures ii) energy conservation = high performance penalty iii) inconvenient for high parallalelization as it increases load imbalance Cheers, -- Szilárd Could you please shed little light on this ? Thanks. Regards, Abhishek -Original Message- From: Mark Abraham mark.j.abra...@gmail.com Sent: 9/5/2014 7:57 PM To: Discussion list for GROMACS users gmx-us...@gromacs.org Subject: Re: [gmx-users] Gromacs 5.0 compilation slower than 4.6.5. What wentwrong ? This cutoff-scheme difference is probably caused by using an .mdp file that does not specify the cutoff scheme, and the default changed in 5.0. grompp issued a note about this, if you go and check it. The change in the -npme choice is a direct consequence of this; the heuristics underlying the splitting choice approximately understand the relative performance characteristics of the two implementations, and you can see that in practice the reported PP/PME balance is decent in each case. There is indeed a large chunk of water (which you can see in group-scheme log files e.g. the line in the FLOP accounting that says NB VdW Elec. [W3-W3,F] dominates the cost), and David's neighbour list is unbuffered. This is indeed the regime where the group scheme might still out-perform the Verlet scheme (depending whether you value buffering in the neighbour list, which you generally should!). Mark On Fri, Sep 5, 2014 at 4:06 PM, Abhi Acharya abhi117acha...@gmail.com wrote: Hello, Is you system solvated with water molecules? The reason I ask is that, in case of the run with 4.6.5 you gromacs has used a group cut-off scheme, whereas 5.0 has used verlet scheme. For system with water molecules, group scheme gives better performance than verlet. For more check out: http://www.gromacs.org/Documentation/Cut-off_schemes Regards, Abhishek Acharya On Fri, Sep 5, 2014 at 7:28 PM, Carsten Kutzner ckut...@gwdg.de wrote: Hi, you might want to use g_tune_pme to find out the optimal number of PME nodes for 4.6 and 5.0. Carsten On 05 Sep 2014, at 15:39, David McGiven davidmcgiv...@gmail.com wrote: What is even more strange is that I tried with 10 pme nodes (mdrun -ntmpi 48 -v -c TEST_md.gro -npme 16), got a 15,8% performance loss and ns/day are very similar : 33 ns/day D. 2014-09-05 14:54 GMT+02:00 David McGiven davidmcgiv...@gmail.com : Hi Abhi, Yes I noticed that imbalance but I thought gromacs knew better than the user how to split PP/PME!! How is it possible that 4.6.5 guesses better than 5.0 ? Anyway, I tried : mdrun -nt 48 -v -c test.out Exits with an error You need to explicitly specify the number of MPI threads (-ntmpi) when using separate PME ranks Then: mdrun -ntmpi 48 -v -c TEST_md.gro -npme 12 Then again 35 ns/day with the warning : NOTE: 8.5 % performance was lost because the PME ranks had less work to do than the PP ranks. You might want to decrease the number of PME ranks or decrease the cut-off and the grid spacing.
Re: [gmx-users] Query regarding the addition of solvent molecule
Hi, Thank you for the suggestions. I did the modifications in the .itp file and the grompp step generated the .tpr file successfully. But now, I am facing problem in the genion step, while adding the NA ions the group 13 (usually SOL for water solvent) is not present there. If I select anyother group like system (Grp-1) its showing some fatal error which is not present in gromacs errors and documentation. I have attached the screenshot of the error page (terminal) and the new .itp file (modified) for your reference. Do I need to add the cyclohexane molecule (CHX) in any of the directories to resolve this error? Kindly need help. https://www.dropbox.com/sh/vkvsr3u2hmh2ft9/AABxNv6VxA1gbSs7h2gkaIfxa?dl=0 On Tue, Sep 9, 2014 at 4:59 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/9/14 7:09 AM, Christina Florina wrote: Hi, Thanks for your suggestions. If the .itp file has error, is there any other way to generate .itp files for the solvents or do i need to write them manually? Because the .itp files I have attached are generated using PRODRG. If I edit the chx.itp file based on the corrections you have told, will it be fine? I am getting the same error for all the 4 solvent files I have generated using PRODRG. I do not get the .itp and .gro files online or tutorials for the organic solvents i am using for my md studies. The only problems I have ever had with PRODRG topologies are charges and charge groups. If you fix those appropriately (charge groups being irrelevant if using the Verlet scheme in Gromacs), that's the only modification you should make. I don't know where all that other stuff came from. I have included the .itp file in both top directory and force field directory. It might be the reason the .gro file could be read in the solvate step. But how to make it in a correct format to proceed with? Solvation doesn't depend on your custom topologies at all. I am new to gromacs using other organic solvents apart from water and default solvents in gromacs package. So, kindly need help how to build an .itp file and .gro file for a solvent and to resolve the issue. Make the changes I indicated in the last message. Read Chapter 5 of the manual for explanations; all of the stuff I pointed out was either (1) syntactically incorrect or (2) not appropriate for the file format. -Justin On Tue, Sep 9, 2014 at 3:38 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/9/14 12:51 AM, Christina Florina wrote: Hi, I have included the link to my dropbox where I have attached my gromacs topology files. Though I have included the cyclohexane itp file in the .top file still I am the same error NO SUCH MOLECULETYPE CHX. SO, Kindly need help in this regard. Thank you in advance. https://www.dropbox.com/sh/vkvsr3u2hmh2ft9/ AABxNv6VxA1gbSs7h2gkaIfxa?dl=0 You have several problems: 1. The #include statement for chx.itp is probably wrong (though I don't know how you're organizing your files), but unless you've put chx.itp in the force field directory, #include gromos43a1.ff/chx.itp is incorrect. 2. The contents of chx.itp are wrong for several reasons. The #ifndef lines are nonsensical and need to be deleted. The #include statement for water needs to be deleted. The [system] and [molecules] levels (which are system-level and thus can only go in a .top) need to be deleted. -Justin On Fri, Sep 5, 2014 at 5:25 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/5/14, 7:10 AM, Christina Florina wrote: Hi, I have included the chx.itp file in the protein.top file already. Checked with the molecule name (CHX) in the .itp file and also in the topology file variable name which matches CHX. But still I am getting the same error. Kindly need help to resolve it. Something doesn't add up. You will need to provide all of your files for download via a file-sharing service to diagnose. A simple #include statement and correct updating of [molecules] is all that is needed. -Justin -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] mean-square displacement
Hello all I would like to plot mean square displacement of hydrogen atoms of protein versus temperature (in order to get dynamical transition temperature). I am using g_msd for this purpose (g_msd -f *_nopbc.xtc -s *.tpr -n index.ndx -o *.xvg) . I am getting following curves as uploded in : http://s903.photobucket.com/user/nidhikatyal1989/media/msd_fig1_zpsc293a5ab.jpg.html How should I plot msd value versus temperature? Is it reasonable enough to take average over 2 ns (linear part) and discard the rest? Moreover, I suspect there is something wrong in the curves too since they are increasing first, reaching saturation and again increasing (last part is unexpected). Actually I am trying to reproduce the results of following paper: THE JOURNAL OF CHEMICAL PHYSICS 130, 135101 2009 , FIG 9 (a) My values are also deviating by larger amount. Am I doing something wrong? Please help. Thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] PBC problem in bilayer system
Dear gromacs users I did MD simulation of my system containing DPPC lipids + water molecule and 4 drug molecules. I saw trajectory file using VMD. Unfortunately, drug molecules jump across the box. How to resolve this PBC problem? which of -pbc options (none, mol, res, atom, nojump, cluster or whole) in trjconv tool is appropriate for my case? Any help will highly appreciated. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PBC problem in bilayer system
Hi, Try -pbc nojump Best, Mike On 09/09/2014 15:11, shahab shariati shahab.shari...@gmail.com wrote: Dear gromacs users I did MD simulation of my system containing DPPC lipids + water molecule and 4 drug molecules. I saw trajectory file using VMD. Unfortunately, drug molecules jump across the box. How to resolve this PBC problem? which of -pbc options (none, mol, res, atom, nojump, cluster or whole) in trjconv tool is appropriate for my case? Any help will highly appreciated. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PBC problem in bilayer system
Also if you want to fix the position on the centre of mass (no rotating or translating) try -pbc nojump Followed by -fit rot+trans Remember to use you new .xtc from your no jump command for the -fit command. Then view in vmd and your molecules will not jump, rotate, or translate around the box. Mike On 09/09/2014 15:12, Michael Carter michael.car...@icr.ac.uk wrote: Hi, Try -pbc nojump Best, Mike On 09/09/2014 15:11, shahab shariati shahab.shari...@gmail.com wrote: Dear gromacs users I did MD simulation of my system containing DPPC lipids + water molecule and 4 drug molecules. I saw trajectory file using VMD. Unfortunately, drug molecules jump across the box. How to resolve this PBC problem? which of -pbc options (none, mol, res, atom, nojump, cluster or whole) in trjconv tool is appropriate for my case? Any help will highly appreciated. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Query regarding the addition of solvent molecule
On 9/9/14 9:41 AM, Christina Florina wrote: Hi, Thank you for the suggestions. I did the modifications in the .itp file and the grompp step generated the .tpr file successfully. But now, I am facing problem in the genion step, while adding the NA ions the group 13 (usually SOL for water solvent) is not present there. If I select anyother group like system (Grp-1) its showing some fatal error which is not present in gromacs errors and documentation. I have attached the screenshot of the error page (terminal) and the new .itp file (modified) for your reference. Do I need to add the cyclohexane molecule (CHX) in any of the directories to resolve this error? Kindly need help. https://www.dropbox.com/sh/vkvsr3u2hmh2ft9/AABxNv6VxA1gbSs7h2gkaIfxa?dl=0 There's no water in your system to replace: [ molecules ] ; Compound#mols Protein_chain_A 1 CHX 3414 I suggest you refer to some tutorial material to understand normal Gromacs workflows and topology organization. There are many linked from the Gromacs website, some of which involve building system with complex/non-water solvents. -Justin On Tue, Sep 9, 2014 at 4:59 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/9/14 7:09 AM, Christina Florina wrote: Hi, Thanks for your suggestions. If the .itp file has error, is there any other way to generate .itp files for the solvents or do i need to write them manually? Because the .itp files I have attached are generated using PRODRG. If I edit the chx.itp file based on the corrections you have told, will it be fine? I am getting the same error for all the 4 solvent files I have generated using PRODRG. I do not get the .itp and .gro files online or tutorials for the organic solvents i am using for my md studies. The only problems I have ever had with PRODRG topologies are charges and charge groups. If you fix those appropriately (charge groups being irrelevant if using the Verlet scheme in Gromacs), that's the only modification you should make. I don't know where all that other stuff came from. I have included the .itp file in both top directory and force field directory. It might be the reason the .gro file could be read in the solvate step. But how to make it in a correct format to proceed with? Solvation doesn't depend on your custom topologies at all. I am new to gromacs using other organic solvents apart from water and default solvents in gromacs package. So, kindly need help how to build an .itp file and .gro file for a solvent and to resolve the issue. Make the changes I indicated in the last message. Read Chapter 5 of the manual for explanations; all of the stuff I pointed out was either (1) syntactically incorrect or (2) not appropriate for the file format. -Justin On Tue, Sep 9, 2014 at 3:38 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/9/14 12:51 AM, Christina Florina wrote: Hi, I have included the link to my dropbox where I have attached my gromacs topology files. Though I have included the cyclohexane itp file in the .top file still I am the same error NO SUCH MOLECULETYPE CHX. SO, Kindly need help in this regard. Thank you in advance. https://www.dropbox.com/sh/vkvsr3u2hmh2ft9/ AABxNv6VxA1gbSs7h2gkaIfxa?dl=0 You have several problems: 1. The #include statement for chx.itp is probably wrong (though I don't know how you're organizing your files), but unless you've put chx.itp in the force field directory, #include gromos43a1.ff/chx.itp is incorrect. 2. The contents of chx.itp are wrong for several reasons. The #ifndef lines are nonsensical and need to be deleted. The #include statement for water needs to be deleted. The [system] and [molecules] levels (which are system-level and thus can only go in a .top) need to be deleted. -Justin On Fri, Sep 5, 2014 at 5:25 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/5/14, 7:10 AM, Christina Florina wrote: Hi, I have included the chx.itp file in the protein.top file already. Checked with the molecule name (CHX) in the .itp file and also in the topology file variable name which matches CHX. But still I am getting the same error. Kindly need help to resolve it. Something doesn't add up. You will need to provide all of your files for download via a file-sharing service to diagnose. A simple #include statement and correct updating of [molecules] is all that is needed. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at
Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 125, Issue 20
Thank you very much! Sincerely nil On Thu, Sep 4, 2014 at 2:51 PM, gromacs.org_gmx-users-requ...@maillist.sys.kth.se wrote: Send gromacs.org_gmx-users mailing list submissions to gromacs.org_gmx-users@maillist.sys.kth.se To subscribe or unsubscribe via the World Wide Web, visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or, via email, send a message with subject or body 'help' to gromacs.org_gmx-users-requ...@maillist.sys.kth.se You can reach the person managing the list at gromacs.org_gmx-users-ow...@maillist.sys.kth.se When replying, please edit your Subject line so it is more specific than Re: Contents of gromacs.org_gmx-users digest... Today's Topics: 1. adding ions in the genion for multimeric proteins (Ambarnil Ghosh) 2. Re: adding ions in the genion for multimeric proteins (rajat desikan) 3. Re: adding ions in the genion for multimeric proteins (Dallas Warren) 4. Re: Structuring as function of z - gmx order (Dallas Warren) 5. Regarding gromacs installation (Sathya) 6. Re: Regarding gromacs installation (Chandan Choudhury) 7. Re: Regarding gromacs installation (Chandan Choudhury) -- Message: 1 Date: Thu, 4 Sep 2014 12:33:34 +0900 From: Ambarnil Ghosh ambargrom...@gmail.com To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] adding ions in the genion for multimeric proteins Message-ID: capn+stt-mjzvwqelxshbzadebfreohjhhto11gfbrqsnqdq...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 Dear users, My protein is a trimer and I want to run md : on binding of a peptide (chain-D) to this trimer (chain-ABC). Therefore, I have four chains. So, when I create topol.top file using pdb2gmx it automatically divide the topology in four *.itp files: topol_Protein_chain_A.itp topol_Protein_chain_B.itp topol_Protein_chain_C.itp topol_Protein_chain_D.itp so, in time of running genion command its required to mention the number of ions to neutralize the protein. Now, each of the protein monomer contains net charge of 2 (qtot) in chain A, B and C. D-peptide have final qtot as 0. Now the question is : Where can I get final qtot for whole system? Is it like that: I have to just sum up all three (2+2+2) and write -nn 6 in genion command ? Or the final qtot value is written in somewhere else in some file, which I missed? I am new to multimeric simulation, any kind of help/lead is much appreciated! Thanks much Sincerely Nil -- Message: 2 Date: Thu, 4 Sep 2014 09:55:14 +0530 From: rajat desikan rajatdesi...@gmail.com To: Discussion list for GROMACS users gmx-us...@gromacs.org Subject: Re: [gmx-users] adding ions in the genion for multimeric proteins Message-ID: CA+d_LwtwDuwF-akbU-kQTSX-r7B49+PkQxMW= nbyw1xnzg1...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 Hi, Use genion -neutral and let gromacs do that hard work. Regards, On Thu, Sep 4, 2014 at 9:03 AM, Ambarnil Ghosh ambargrom...@gmail.com wrote: Dear users, My protein is a trimer and I want to run md : on binding of a peptide (chain-D) to this trimer (chain-ABC). Therefore, I have four chains. So, when I create topol.top file using pdb2gmx it automatically divide the topology in four *.itp files: topol_Protein_chain_A.itp topol_Protein_chain_B.itp topol_Protein_chain_C.itp topol_Protein_chain_D.itp so, in time of running genion command its required to mention the number of ions to neutralize the protein. Now, each of the protein monomer contains net charge of 2 (qtot) in chain A, B and C. D-peptide have final qtot as 0. Now the question is : Where can I get final qtot for whole system? Is it like that: I have to just sum up all three (2+2+2) and write -nn 6 in genion command ? Or the final qtot value is written in somewhere else in some file, which I missed? I am new to multimeric simulation, any kind of help/lead is much appreciated! Thanks much Sincerely Nil -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- Message: 3 Date: Thu, 04 Sep 2014 03:56:18 + From: Dallas Warren dallas.war...@monash.edu To: gmx-us...@gromacs.org gmx-us...@gromacs.org Subject: Re: [gmx-users] adding ions in the genion for multimeric proteins Message-ID:
Re: [gmx-users] Cuda CC 2.0 restrictions
Hi, Is this rather large box a system that can actually be simulated with a useful speed on a single Fermi GPU? Even with 5 fs time-step you won't get much more than 1-1.5 ns/day on a fast Fermi GPU like a GTX 580. Given that you are quite a bit above the limit, unless you are using a quite large nstlist, you may not be able to decrease it enough to fit the system on the GPU. What you can do instead is to use domain-decomposition and start multiple ranks per GPU. In your case two-way DD should be enough. Cheers, -- Szilárd On Fri, Sep 5, 2014 at 11:24 PM, Mirco Wahab mirco.wa...@chemie.tu-freiberg.de wrote: I've run into a problem with an older card (GTX-580) which is CC 2.0. On a larger box size, mdrun stops with: Fatal error: Watch out, the input system is too large to simulate! The number of nonbonded work units (=number of super-clusters) exceeds themaximum grid size in x dimension (86276 65535)! This seems to refer to the CUDA grid of thread blocks per dimension, limitation specific for CC below 3.0 (I know this system worked already on a CC 3.0 device). My question: can this grid count calculated by mdrun be manipulated somehow by mdp options (nstlist, rvdw, rlist)? Thanks, M. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Using GROMACS to find the net charge on a Protein
Dear Users I am trying to find the net charge at the physiological pH value for a protein molecule (Thrombin) in my case and am wondering if it is possible to use GROMACS for doing it. I am very new to GROMACS and at present I have been going through the tutorials by Dr. Lemkul. I have seen that the topology file generated by pdb2gmx contains the total electron charge value for a molecule. I was wondering if this can be used to get the charge value for Thrombin at physiological pH. Thanks Regards Agnivo Gosai Graduate Student Mechanical Engineering Iowa State University -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] use of -t nvt.cpt option in NPT equilibration
Hi, Can someone please explain if it is necessary to use the -t flag during NPT equilibration? The following command is mentioned in the lysozyme tutorial: $ grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr whereas , I have found the command without the -t flag in another tutorial: grompp -v -f npt.mdp -c protein-NVT.gro -p protein.top -o protein-NPT.tpr Thanking in advance, regards, ansuman -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] use of -t nvt.cpt option in NPT equilibration
Hi Ansuman, That is optional. Regards, Vijayan.R On Tue, Sep 9, 2014 at 4:38 PM, Ansuman Biswas ansu...@physics.iisc.ernet.in wrote: Hi, Can someone please explain if it is necessary to use the -t flag during NPT equilibration? The following command is mentioned in the lysozyme tutorial: $ grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr whereas , I have found the command without the -t flag in another tutorial: grompp -v -f npt.mdp -c protein-NVT.gro -p protein.top -o protein-NPT.tpr Thanking in advance, regards, ansuman -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] use of -t nvt.cpt option in NPT equilibration
On 9/9/14 5:09 PM, R.S.K.Vijayan wrote: Hi Ansuman, That is optional. Generally speaking, no, it's not. The real truth lies in what the .mdp settings are and what the intent of NPT is. If you don't pass the .cpt file to grompp -t, you stand to lose much (or all) of the previous state information, thus introducing discontinuities. Rule of thumb: preserve the previous ensemble unless you have a very good reason to ignore or re-create it. -Justin Regards, Vijayan.R On Tue, Sep 9, 2014 at 4:38 PM, Ansuman Biswas ansu...@physics.iisc.ernet.in wrote: Hi, Can someone please explain if it is necessary to use the -t flag during NPT equilibration? The following command is mentioned in the lysozyme tutorial: $ grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr whereas , I have found the command without the -t flag in another tutorial: grompp -v -f npt.mdp -c protein-NVT.gro -p protein.top -o protein-NPT.tpr Thanking in advance, regards, ansuman -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Using GROMACS to find the net charge on a Protein
On 9/9/14 3:51 PM, Agnivo Gosai wrote: Dear Users I am trying to find the net charge at the physiological pH value for a protein molecule (Thrombin) in my case and am wondering if it is possible to use GROMACS for doing it. I am very new to GROMACS and at present I have been going through the tutorials by Dr. Lemkul. I have seen that the topology file generated by pdb2gmx contains the total electron charge value for a molecule. I was wondering if this can be used to get the charge value for Thrombin at physiological pH. Gromacs will assume canonical protonation states at pH 7 for all residues (unless you reassign them manually, in which case there's really no point in running pdb2gmx because you know the answer). Whether or not this assumption is valid depends on the actual pKa values of the constituent amino acids. There are much more rigorous ways to calculate the net charge of a protein; I'd suggest you look at other servers and methods. There is a huge community of people who do pKa predictions. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Using GROMACS to find the net charge on a Protein
Quick answer is no. In fact, that's really not what (standard) molecular dynamics is for. You need a constant-pH MD method for that. Read this to get a bit more acquainted with the subject (might be overkill for you, because I doubt this is what you want/need): http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation Either way, if you really don't need a lot of detail and an approximate protein net charge will do, why not just look at the pKa's of each amino acid and try to work out what the net charge would be for a given pH? It's a quite simple exercise to do with pen and paper and you're never going to be that far off from reality. If the protein is too large, just script it or search the web for a tool to do such. I bet there are a few. P.S. no.1: pdb2gmx knows nothing about pH. It will set the most likely charge for each amino acid at pH 7. It's as accurate as the pen and paper method I suggested. This tool's purpose has little or nothing to do with what you need. P.S. no.2: Have you done your literary research properly? I never worked with thrombin but it doesn't sound very exotic. I bet there are some titration studies of it. Best regards, João Henriques On Tue, Sep 9, 2014 at 9:51 PM, Agnivo Gosai agnivo2...@gmail.com wrote: Dear Users I am trying to find the net charge at the physiological pH value for a protein molecule (Thrombin) in my case and am wondering if it is possible to use GROMACS for doing it. I am very new to GROMACS and at present I have been going through the tutorials by Dr. Lemkul. I have seen that the topology file generated by pdb2gmx contains the total electron charge value for a molecule. I was wondering if this can be used to get the charge value for Thrombin at physiological pH. Thanks Regards Agnivo Gosai Graduate Student Mechanical Engineering Iowa State University -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] g_energy reporting 0.0000 interaction energy between energy groups in GPU run?
Dear users, I did some simulations of organic molecules in solution to study how they interact, but I'm facing some problems and your help would be greatly appreciated. Consider the following case: I simulated two copies of molecule AcO starting from a structure in which they are non-covalently interacting. I'm using the AMBER99 forcefield with GAFF. I've confirmed by visual inspection that the molecules are interacting with each other, i.e. they didn't separate during the simulation. Additionally, I've specified the energy groups aco_1, aco_2, SOL, Ion in the original MD tpr. The problem is that g_energy reports all aco_1-aco_2 energy terms as exactly 0.00. The energy terms are OK. This was only an example. I actually simulated 2, 3 and 4 copies of interacting molecules in different ways and this happens in all cases. These results were obtained using GPUs. I used the same .tpr to rerun the .xtc on CPUs only and now the aco_1-aco_2 energy terms are OK. In both cases I used GROMACS 4.6.6. I've searched the list but found nothing. Is this a problem/bug? Am I doing something wrong with the GPUs? Thank you in advance, Leandro -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g_energy reporting 0.0000 interaction energy between energy groups in GPU run?
On 9/9/14 9:09 PM, Leandro Bortot wrote: Dear users, I did some simulations of organic molecules in solution to study how they interact, but I'm facing some problems and your help would be greatly appreciated. Consider the following case: I simulated two copies of molecule AcO starting from a structure in which they are non-covalently interacting. I'm using the AMBER99 forcefield with GAFF. I've confirmed by visual inspection that the molecules are interacting with each other, i.e. they didn't separate during the simulation. Additionally, I've specified the energy groups aco_1, aco_2, SOL, Ion in the original MD tpr. The problem is that g_energy reports all aco_1-aco_2 energy terms as exactly 0.00. The energy terms are OK. This was only an example. I actually simulated 2, 3 and 4 copies of interacting molecules in different ways and this happens in all cases. These results were obtained using GPUs. I used the same .tpr to rerun the .xtc on CPUs only and now the aco_1-aco_2 energy terms are OK. In both cases I used GROMACS 4.6.6. I've searched the list but found nothing. Is this a problem/bug? Am I doing something wrong with the GPUs? Multiple energygrps are not supported on GPU. This should be disabled in 5.0.1, and if not, hopefully the next release, as it is a known issue. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g_energy reporting 0.0000 interaction energy between energy groups in GPU run?
Thank you for your quick answer, Justin. I'll make new .edr files using only CPUs. Best regards, Leandro On Tue, Sep 9, 2014 at 10:11 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/9/14 9:09 PM, Leandro Bortot wrote: Dear users, I did some simulations of organic molecules in solution to study how they interact, but I'm facing some problems and your help would be greatly appreciated. Consider the following case: I simulated two copies of molecule AcO starting from a structure in which they are non-covalently interacting. I'm using the AMBER99 forcefield with GAFF. I've confirmed by visual inspection that the molecules are interacting with each other, i.e. they didn't separate during the simulation. Additionally, I've specified the energy groups aco_1, aco_2, SOL, Ion in the original MD tpr. The problem is that g_energy reports all aco_1-aco_2 energy terms as exactly 0.00. The energy terms are OK. This was only an example. I actually simulated 2, 3 and 4 copies of interacting molecules in different ways and this happens in all cases. These results were obtained using GPUs. I used the same .tpr to rerun the .xtc on CPUs only and now the aco_1-aco_2 energy terms are OK. In both cases I used GROMACS 4.6.6. I've searched the list but found nothing. Is this a problem/bug? Am I doing something wrong with the GPUs? Multiple energygrps are not supported on GPU. This should be disabled in 5.0.1, and if not, hopefully the next release, as it is a known issue. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] protein-ligand complex by gromacs
did you center everything, or are you just looking at it in VMD? Gesendet:Montag, 08. September 2014 um 18:30 Uhr Von:Mahboobeh Eslami mahboobeh.esl...@yahoo.com An:gmx-us...@gromacs.org gmx-us...@gromacs.org Betreff:[gmx-users] protein-ligand complex by gromacs hi GMX users i have simulated the protein-ligand complex by gromacs. Ive repeated the simulation twice but i have get very different results. in one of the simulations ligand separated from protein and stayed in the center of box. Ive checked all of the input files and the steps , but I did not understand why this happened. Please help me . Thank you for your kindness -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Cant post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g_mindist for hydrophobic interactions
you should go down the list and use all the tools, and use some from seperate software. In my experience, the trjconv gets rid of say 4-5 crazy single points in a graph based on a single point where one of the atoms or residues involved moves between planes, which averidge out in a gaussian distribution, but it removes these. Somone e.lse here probably has better contributions though. It is hard to say without seeing the raw data though. Stephan Watkins Gesendet:Montag, 08. September 2014 um 10:25 Uhr Von:Ca C. devi...@hotmail.com An:gromacs.org_gmx-users@maillist.sys.kth.se gromacs.org_gmx-users@maillist.sys.kth.se Betreff:[gmx-users] g_mindist for hydrophobic interactions Dear All, I have to verify if some hydrophobic residues, during the simulation, conserve their interactions and make a cross talk for receptors transactivation. Is g_mindist a good tool for this purpose? Do you have more suggestions? Moreover, should I use trjconv for pbc treatment before running g_mindist? Thank you in advance -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Cant post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Contact angle measurement on a flat surface
Dear all,I would like to know what are the methods I could use to measure/plot the contact angle of a water nanodroplet on flat graphene.Is there a script or tool in GROMACS that can perform the contact angle calculation? I am aware that the commonly used Young's equation does not apply here, since the droplet sizes will be in nanoscale.The modified Young-Dupre's equation, and other plotting methods such as the graphical binning approach by Werder et al. J. Phys. Chem. B 107, 1345-1352 (2003), and the algorithm method by Ingebrigtsen and Toxvaerd, J. Phys. Chem. C 111, 8518 (2007) provided some theory on the calculation, but I would like to know about the technical steps on doing the measurement.Any feedback is greatly appreciated.Thank you in advance.Regards,Kester -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
