Re: [gmx-users] what does it mean by 'started mdrun on node 0'
Hi Yihua Zhou, Step Time Lambda 00.00.0 Energies (kJ/mol) Bond G96AngleProper Dih.LJ (SR) Coulomb (SR) 4.19801e+051.40206e+033.49599e+038.36580e+208.17307e+04 PotentialKinetic En. Total EnergyTemperature Pressure (bar) 8.36580e+20infinfinfinf This is the relevant information from your log file. As you can see there are several terms at infinite. That indicates there's a problem. The short-range Lennard-Jones is quite high. Probably you have overlaps in your system. Did you check the system before running, also making sure that the PBC are set correctly and not cause overlaps? Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- 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] MM-GB/SA analysis in Gromacs
Dear gmx-users, I ran several MD simulations using Gromacs 4.5.4 version, and now I'd need to calculate binding free energies using the MM-GBSA method. I searched through the manual and through the gmx-users archive, but I didn't find a way to do it. I found an old post in which it appeared that in the version 4.5 this possibility would have been available (http://lists.gromacs.org/pipermail/gmx-users/2010-July/052302.html), but it seems to me that this kind of analysis has not been implemented yet. In another more recent post, I see that somebody has used mdrun -rerun in order to perform calculations, but I don't understand the correct procedure to use (apart from the suggestion of using .trr instead of .xtc files in order to avoid errors). Does anyone have suggestions in order to do this analysis with Gromacs trajectories, before I make these calculations with another program? Many thanks in advance and best regards Anna -- __ Anna Marabotti, Ph.D. Assistant Professor Department of Chemistry and Biology University of Salerno Via Ponte don Melillo 84084 Fisciano (SA) Italy Phone: +39 089 969583 Fax: +39 089 969603 E-mail: amarabo...@unisa.it Skype: annam1972 When a man with a gun meets a man with a pen, the man with the gun is a dead man (Roberto Benigni, about Roberto Saviano) -- 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] Hbonds between Adenine and Thymine
Hi, A general note: make_ndx and index files are not magical in any way. You can usually construct an index group from e.g. a pdb file with awk. It's just lists of atom indices. Best, Erik 28 nov 2012 kl. 22.33 skrev Justin Lemkul: On 11/28/12 3:43 PM, Hovakim Grabski wrote: Dear Gromacs users, I set a simulation of 26 base pairs of DNA with Ethidium Bromide for 5 ns. After a while Thymine rotated for about 70 degrees and then returned to its initial position. I wanted to find out hbonds between Adenine and Thymine but with make_ndx things don't work so well. How can I select Adenine from one strand and Thymine from the other strand and then run g_hbond ? You can use make_ndx to select any residues you want. You'll have to describe exactly what you did that produced insufficient results. Saying it didn't work well doesn't tell us anything, because it is in fact quite easy to produce usable index groups. -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 --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- 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] error during nvt equilibration
On 11/29/12 12:40 AM, Shine A wrote: Sir, I am studying the dynamics of membrane proteins using KALP-15 in DPPC. Now doing nvt equilibration and created index.ndx by using make_ndx. During this step I selected 16/14 and 1/13.The next step (grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr) getting error like this Fatal error: Group SOL_CL not found in indexfile. Maybe you have non-default goups in your .mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. why this error? Can you give a solution to overcome it? You're using a group called SOL_CL in the .mdp file, but one is not found in the .ndx file. If indeed you used 16/14 to make the necessary index group, that is wrong. The syntax is a pipe (|) to merge groups, not a slash (/). -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] gromacs 4.5.5 Do_dssp segment fault
Thanks for your help!I will try . -- xiaohong --Original-- From: "Justin Lemkul"jalem...@vt.edu; Date: Thu, Nov 29, 2012 10:43 AM To: "Discussion list for GROMACS users"gmx-users@gromacs.org; Subject: Re: [gmx-users] gromacs 4.5.5 Do_dssp segment fault On 11/28/12 9:21 PM, Kdead wrote: When I use the Do_dssp module to collect the data from --.trr ,It report segment fault. The other common module is normol.WHY?? Thanks!The input options in the DSSP executable changed. This is a known problem and has been around for a long time. Your options are:1. Obtain an old version of DSSP2. Apply the patch described in the mailing list archive or otherwise install the development version via git3. Wait for the first beta release of version 4.6, where this problem is fixed (should be released very soon)-Justin-- Justin A. Lemkul, Ph.D.Research ScientistDepartment of BiochemistryVirginia TechBlacksburg, VAjalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin-- gmx-users mailing list gmx-users@gromacs.orghttp://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] Hbonds between Adenine and Thymine
Please keep the discussion on the gmx-users list. On 11/29/12 6:12 AM, Hovakim Grabski wrote: Dear Justin, When I try to select 10DA residue from one strand and 17DT from the other strand,I type r10 and r17 and both select 64 atoms, after r26 it selects water molecules. You can easily check (using a text editor) which atoms make_ndx is choosing. In theory, your approach is correct and very straightforward. Can you please provide? 1. Your exact make_ndx command 2. A few lines from residue 10DA of whatever coordinate file you're using 3. The index group produced from residue 10 Did you renumber the file at any point, for instance, with pdb2gmx? That is, whatever started out as residue 10 may not still be numbered as such in the topology and any resulting coordinate files produced from the simulation. Without knowing exactly what you're using as make_ndx input, it's hard to track down what's going on. -Justin And then I check for Hbonds with g_hbond I get 3 Hbonds, but between A and T they form 2 Hbonds? It seems I'm doing something wrong. What can I do in this case? Thanks in advance, Best regards, Hovakim *От:* Justin Lemkul jalem...@vt.edu *Кому:* Hovakim Grabski hovakim_grab...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org *Отправлено:* четверг, 29 ноября 2012 1:33 *Тема:* Re: [gmx-users] Hbonds between Adenine and Thymine On 11/28/12 3:43 PM, Hovakim Grabski wrote: Dear Gromacs users, I set a simulation of 26 base pairs of DNA with Ethidium Bromide for 5 ns. After a while Thymine rotated for about 70 degrees and then returned to its initial position. I wanted to find out hbonds between Adenine and Thymine but with make_ndx things don't work so well. How can I select Adenine from one strand and Thymine from the other strand and then run g_hbond ? You can use make_ndx to select any residues you want. You'll have to describe exactly what you did that produced insufficient results. Saying it didn't work well doesn't tell us anything, because it is in fact quite easy to produce usable index groups. -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 -- 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] MM-GB/SA analysis in Gromacs
Dear all, I would like to bring to your attention this paper http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0046902 in which we made a tool to perform MM/PBSA binding free energy calculation in automatic fashion, using torque/pbs parallel system implemented in most clusters. The input of the tools are just the xtc trajectory, the tpr and eventually the index file. It does perform the computational alanine scanning (CAS) too. The tool is available upon request. Further details on the paper. Regards, and On 11/29/2012 10:42 AM, Anna Marabotti wrote: Dear gmx-users, I ran several MD simulations using Gromacs 4.5.4 version, and now I'd need to calculate binding free energies using the MM-GBSA method. I searched through the manual and through the gmx-users archive, but I didn't find a way to do it. I found an old post in which it appeared that in the version 4.5 this possibility would have been available (http://lists.gromacs.org/pipermail/gmx-users/2010-July/052302.html), but it seems to me that this kind of analysis has not been implemented yet. In another more recent post, I see that somebody has used mdrun -rerun in order to perform calculations, but I don't understand the correct procedure to use (apart from the suggestion of using .trr instead of .xtc files in order to avoid errors). Does anyone have suggestions in order to do this analysis with Gromacs trajectories, before I make these calculations with another program? Many thanks in advance and best regards Anna -- - Andrea Spitaleri PhD Dulbecco Telethon Institute c/o Fondazione Centro San Raffaele Centro di Genomica Traslazione e Bioinformatica Biomolecular NMR Laboratory Dibit2 Basilica 3A2 Via Olgettina 58 20132 Milano Italy Tel: 0039-0226434348 Fax: 0039-0226434153 http://sites.google.com/site/andreaspitaleri/ http://www.linkedin.com/in/andreaspitaleri - -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] error during mdrun
Sir, I am studying the dynamics of membrane proteins using KALP-15 in DPPC. Now doing nvt equilibration.During mdrun (mdrun -deffnm nvt) getting error like this Fatal error: 6 particles communicated to PME node 1 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated. why this error? How can I solve this? -- 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] error during mdrun
On 11/29/12 7:49 AM, Shine A wrote: Sir, I am studying the dynamics of membrane proteins using KALP-15 in DPPC. Now doing nvt equilibration.During mdrun (mdrun -deffnm nvt) getting error like this Fatal error: 6 particles communicated to PME node 1 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated. why this error? How can I solve this? http://www.gromacs.org/Documentation/Errors#X_particles_communicated_to_PME_node_Y_are_more_than_a_cell_length_out_of_the_domain_decomposition_cell_of_their_charge_group The website has troubleshooting tips by following the link above, and the mailing list archive has about a million posts on this topic too. Surely something will be of use. -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] Electrostatic field in atoms - GROMACS is not reading table interaction functions for bonded interactions
Dear GROMACS users, We are trying to determine the electric fields at the C and N atoms in a protein. To do so, we thought of performing a one step energy minimization with the Lennard-Jones as well as the bonded interactions turned off, in order to get only the coulomb forces. For that, according to www.gromacs.org/Documentation/How-tos/Tabulated_Potentials , we made a table (table.xvg) in which the Lennard-Jones potential was set to zero and we also made three tables (table_b1.xvg, table_a5.xvg and table_d5.xvg) according to section 4.2.13 of the Manual (Tabulated interaction functions), in which the f(x)=0 for the whole range of distances, angles, dihedrals present in the simulation box. The numbers 1, 5, 2 correspond to the function number referred to in the topology file. For example for the bonds interaction, in the topology file we have: [ bonds ] ; aiaj functc0c1c2c3 1 2 1 1 3 1 1 4 1 1 5 1 5 6 1 . . . so we named the table table_b1.xvg. We changed the run.mdp file as follows: vdw-type = User coulombtype = PME-User And then we try to run it using: mdrun -v -deffnm run.tpr When checking the energy contribution using g_energy, Lennard-Jones contribution was indeed zero, but for the bonded interactions this is not the case: Energy Average Err.Est. RMSD Tot-Drift --- U-B 18180.1 --276.416 -540.638 (kJ/mol) Proper Dih. 11732.3 --27.6829 -54.0396 (kJ/mol) Improper Dih. 1027.26 --47.1598 -91.7097 (kJ/mol) LJ-14 0 -- 0 0 (kJ/mol) LJ (SR) 0 -- 0 0 (kJ/mol) We though that maybe the tables for the bonded interactions were not taken, so we tried: mdrun -v -tableb table_b1.xvg table_a5.xvg table_d2.xvg -deffnm run.tpr But it also did not work. We are not sure whether the problem is in the table definition, the way of running the program, the run type, the name of the tables, or if there should be some other modifications in the *mdp file. We would be very grateful if anyone could help us out here. Thanks a lot in advance and with kind regards, Ariana-- 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] Electrostatic field in atoms - GROMACS is not reading table interaction functions for bonded interactions
On 11/29/12 8:18 AM, Ariana Torres Knoop wrote: Dear GROMACS users, We are trying to determine the electric fields at the C and N atoms in a protein. To do so, we thought of performing a one step energy minimization with the Lennard-Jones as well as the bonded interactions turned off, in order to get only the coulomb forces. For that, according to www.gromacs.org/Documentation/How-tos/Tabulated_Potentials , we made a table (table.xvg) in which the Lennard-Jones potential was set to zero and we also made three tables (table_b1.xvg, table_a5.xvg and table_d5.xvg) according to section 4.2.13 of the Manual (Tabulated interaction functions), in which the f(x)=0 for the whole range of distances, angles, dihedrals present in the simulation box. The numbers 1, 5, 2 correspond to the function number referred to in the topology file. For example for the bonds interaction, in the topology file we have: [ bonds ] ; aiaj functc0c1c2c3 1 2 1 1 3 1 1 4 1 1 5 1 5 6 1 . . . so we named the table table_b1.xvg. We changed the run.mdp file as follows: vdw-type = User coulombtype = PME-User And then we try to run it using: mdrun -v -deffnm run.tpr When checking the energy contribution using g_energy, Lennard-Jones contribution was indeed zero, but for the bonded interactions this is not the case: Energy Average Err.Est. RMSD Tot-Drift --- U-B 18180.1 --276.416 -540.638 (kJ/mol) Proper Dih. 11732.3 --27.6829 -54.0396 (kJ/mol) Improper Dih. 1027.26 --47.1598 -91.7097 (kJ/mol) LJ-14 0 -- 0 0 (kJ/mol) LJ (SR) 0 -- 0 0 (kJ/mol) We though that maybe the tables for the bonded interactions were not taken, so we tried: mdrun -v -tableb table_b1.xvg table_a5.xvg table_d2.xvg -deffnm run.tpr But it also did not work. We are not sure whether the problem is in the table definition, the way of running the program, the run type, the name of the tables, or if there should be some other modifications in the *mdp file. We would be very grateful if anyone could help us out here. I think the problem comes from the fact that the function types you are specifying in the topology correspond to actual potentials and thus the tables are being ignored. Per Table 5.5, it seems that any value for the table is acceptable (n = 0) but using numbers corresponding to actual function types may not work. The specified format also requires that both the table number and force constant (k) be specified in the topology, but the [bonds] section you show above has no value of k and the function type corresponds to a simple harmonic bond. There is no bond energy in the output, which suggests you are using constraints - is that the case? -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:Energy landscapes
Dear All, I remember a post in the last couple months but cant find it. In any case, by searching through van der groot et alls. papers, the -xmin, -xmax, -dim and -ngrid options third point, example: -xmin 3 3 3 -xmax 3 3 3 is for reading in the output 3d (projections on V1, V2, V3 or first three vectors, and is output as xyz points in a pdb file. This can be read into various ploting or even pymol/vmd to illustrate the projection on a PCA of 3 dimensions. From the lit it is supposed to show 2 or more conformational states, and a number of intermediary states in between (overall just a 3d PCA graph). If I am wrong please correct me, but this is what the output for me was doing, and I personally prefer the 2D, as its easier to illustrait (as images in 3d lack the necessary rotation to show everything in a static image). Sincerely, Stephan Watkins -- 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] g_tune_pme for multiple nodes
Hi Carsten, Thanks for your suggestion. I did try to pass to total number of cores with the np flag to the g_tune_pme, but it didnot help. Hopefully I am doing something silliy. I have pasted the snippet of the PBS script. #!/bin/csh #PBS -l nodes=2:ppn=12:twelve #PBS -N bilayer_tune cd $PBS_O_WORKDIR export MDRUN=/cm/shared/apps/gromacs/4.5.5/single/bin/mdrun_mpi_4.5.5 mpirun -np $NPROCS g_tune_pme_4.5.5 -np 24 -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log -nice 0 Then I submit the script using qsub. When I login to the compute nodes there I donot find and mdrun executable running. I also tried using nodes=1 and np 12. It didnot work through qsub. Then I logged in to the compute nodes and executed g_tune_pme_4.5.5 -np 12 -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log -nice 0 It worked. Also, if I just use $g_tune_pme_4.5.5 -np 12 -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log -nice 0 g_tune_pme executes on the head node and writes various files. Kindly let me know what am I missing when I submit through qsub. Thanks Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Mon, Sep 3, 2012 at 3:31 PM, Carsten Kutzner ckut...@gwdg.de wrote: Hi Chandan, g_tune_pme also finds the optimal number of PME cores if the cores are distributed on multiple nodes. Simply pass the total number of cores to the -np option. Depending on the MPI and queue environment that you use, the distribution of the cores over the nodes may have to be specified in a hostfile / machinefile. Check g_tune_pme -h on how to set that. Best, Carsten On Aug 28, 2012, at 8:33 PM, Chandan Choudhury iitd...@gmail.com wrote: Dear gmx users, I am using 4.5.5 of gromacs. I was trying to use g_tune_pme for a simulation. I intend to execute mdrun at multiple nodes with 12 cores each. Therefore, I would like to optimize the number of pme nodes. I could execute g_tune_pme -np 12 md.tpr. But this will only find the optimal PME nodes for single nodes run. How do I find the optimal PME nodes for multiple nodes. Any suggestion would be helpful. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- 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 -- 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 http://www3.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- 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
AW: [gmx-users] g_tune_pme for multiple nodes
-Ursprüngliche Nachricht- Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] Im Auftrag von Chandan Choudhury Gesendet: Donnerstag, 29. November 2012 15:31 An: Discussion list for GROMACS users Betreff: Re: [gmx-users] g_tune_pme for multiple nodes Hi Carsten, Thanks for your suggestion. I did try to pass to total number of cores with the np flag to the g_tune_pme, but it didnot help. Hopefully I am doing something silliy. I have pasted the snippet of the PBS script. #!/bin/csh #PBS -l nodes=2:ppn=12:twelve #PBS -N bilayer_tune cd $PBS_O_WORKDIR export MDRUN=/cm/shared/apps/gromacs/4.5.5/single/bin/mdrun_mpi_4.5.5 mpirun -np $NPROCS g_tune_pme_4.5.5 -np 24 -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log -nice 0 Hi, Don't start an MPI process. Run: g_tune_pme_4.5.5 -np 24 -s md0-200.tpr -c tune.pdb -x and everything should work fine. /Flo Then I submit the script using qsub. When I login to the compute nodes there I donot find and mdrun executable running. I also tried using nodes=1 and np 12. It didnot work through qsub. Then I logged in to the compute nodes and executed g_tune_pme_4.5.5 -np 12 - s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log -nice 0 It worked. Also, if I just use $g_tune_pme_4.5.5 -np 12 -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log -nice 0 g_tune_pme executes on the head node and writes various files. Kindly let me know what am I missing when I submit through qsub. Thanks Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Mon, Sep 3, 2012 at 3:31 PM, Carsten Kutzner ckut...@gwdg.de wrote: Hi Chandan, g_tune_pme also finds the optimal number of PME cores if the cores are distributed on multiple nodes. Simply pass the total number of cores to the -np option. Depending on the MPI and queue environment that you use, the distribution of the cores over the nodes may have to be specified in a hostfile / machinefile. Check g_tune_pme -h on how to set that. Best, Carsten On Aug 28, 2012, at 8:33 PM, Chandan Choudhury iitd...@gmail.com wrote: Dear gmx users, I am using 4.5.5 of gromacs. I was trying to use g_tune_pme for a simulation. I intend to execute mdrun at multiple nodes with 12 cores each. Therefore, I would like to optimize the number of pme nodes. I could execute g_tune_pme -np 12 md.tpr. But this will only find the optimal PME nodes for single nodes run. How do I find the optimal PME nodes for multiple nodes. Any suggestion would be helpful. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- 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 -- 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 http://www3.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- 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] Potential energy from a previous configuration mismatch
Dear Gromacs friends, I am running some simulations of a hexane/ethanol mixture in a box, using a United-Atom OPLS model. My Gromacs version is the 4.5.5. I fill the simulation box with genbox (I have also used an equilibrated pdb file generated by other simulation code), and I run a energy minimization simulation, wich gives the following energies for the final configuration: Energies (kJ/mol) Angle Fourier Dih. LJ-14 Coulomb-14LJ (SR) 6.62915e+005.17493e+02 -2.61388e+01 0.0e+00 -4.01422e+03 Disper. corr. Coulomb (SR) RF excl. Potential Pres. DC (bar) -9.65799e+010.0e+000.0e+00 -3.61282e+030.0e+00 Potential Energy = -3.6128213e+03 Maximum force = 2.7169607e+01 on atom 541 Norm of force = 3.9986315e+00 I take the final configuration, and using exactly the same force field definition and simulation parameters (cutoff radious, electrostatic method, etc), I start a molecular dynamics simulation in the NVE ensemble. No matter what I do, I always have a blow-up problem. I have checked all the points that could be giving the problem, in particular the ones given here: http://www.gromacs.org/Documentation/Terminology/Blowing_Up and I have also tried to modify one by one different parameters, but I never succeed to obtain a running simulation. I have seen that I always have a much larger energy at the beginning of the simulation than the energy at the end of the minimization: Energies (kJ/mol) Angle Fourier Dih. LJ-14 Coulomb-14LJ (SR) 5.43743e+042.06120e+036.02532e+01 0.0e+001.62817e+07 Disper. corr. Coulomb (SR) RF excl. PotentialKinetic En. -9.65799e+010.0e+000.0e+00 1.63381e+071.65906e+10 Total EnergyTemperature Pres. DC (bar) Pressure (bar) Constr. rmsd 1.66069e+10 but the potential energy should be exactly the same in both cases, as it only depends on the atomic positions. Anybody can tell me what I am doing wrong? 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] g_tune_pme for multiple nodes
Hi Chandan, On Nov 29, 2012, at 3:30 PM, Chandan Choudhury iitd...@gmail.com wrote: Hi Carsten, Thanks for your suggestion. I did try to pass to total number of cores with the np flag to the g_tune_pme, but it didnot help. Hopefully I am doing something silliy. I have pasted the snippet of the PBS script. #!/bin/csh #PBS -l nodes=2:ppn=12:twelve #PBS -N bilayer_tune cd $PBS_O_WORKDIR export MDRUN=/cm/shared/apps/gromacs/4.5.5/single/bin/mdrun_mpi_4.5.5 from here on you job file should read: export MPIRUN=`which mpirun` g_tune_pme_4.5.5 -np $NPROCS -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log mpirun -np $NPROCS g_tune_pme_4.5.5 -np 24 -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log -nice 0 this way you will get $NPROCS g_tune_pme instances, each trying to run an mdrun job on 24 cores, which is not what you want. g_tune_pme itself is a serial program, it just spawns the mdrun's. Carsten Then I submit the script using qsub. When I login to the compute nodes there I donot find and mdrun executable running. I also tried using nodes=1 and np 12. It didnot work through qsub. Then I logged in to the compute nodes and executed g_tune_pme_4.5.5 -np 12 -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log -nice 0 It worked. Also, if I just use $g_tune_pme_4.5.5 -np 12 -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log -nice 0 g_tune_pme executes on the head node and writes various files. Kindly let me know what am I missing when I submit through qsub. Thanks Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Mon, Sep 3, 2012 at 3:31 PM, Carsten Kutzner ckut...@gwdg.de wrote: Hi Chandan, g_tune_pme also finds the optimal number of PME cores if the cores are distributed on multiple nodes. Simply pass the total number of cores to the -np option. Depending on the MPI and queue environment that you use, the distribution of the cores over the nodes may have to be specified in a hostfile / machinefile. Check g_tune_pme -h on how to set that. Best, Carsten On Aug 28, 2012, at 8:33 PM, Chandan Choudhury iitd...@gmail.com wrote: Dear gmx users, I am using 4.5.5 of gromacs. I was trying to use g_tune_pme for a simulation. I intend to execute mdrun at multiple nodes with 12 cores each. Therefore, I would like to optimize the number of pme nodes. I could execute g_tune_pme -np 12 md.tpr. But this will only find the optimal PME nodes for single nodes run. How do I find the optimal PME nodes for multiple nodes. Any suggestion would be helpful. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- 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 -- 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 http://www3.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- 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 -- 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 http://www.mpibpc.mpg.de/grubmueller/kutzner -- 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] About Diffusion of Water towards Protein in ceter of box
Dear Justin, Thank you for your Previous Reply To avoid the Diffusion of Water You Suggested me s follows The better approach would be a position restrain along the z-axis only, allowing the lipids to perhaps re-orient and pack a bit better, followed by NVT equilibration in the absence of any restraints on water. According to your Suggestion Should i Do the Two times Equilibration With restraint On water only in First NVT equilibration followed by another NVT equilibration without restraint on Water But Only With Lipids ? My Question is Can i simultaneously use Restraint for water and Lipids in Single NVT equilibration ? If i can My NVT equilibration is Successful (means No Diffusion of Water in the Tail Part.) But After That When I do NPT Equilibration There is Diffusion Of Some Water molecules Towards the protein in the center of box Not towards Tail of Lipids Is this Behavior is ODD or Normal ? If it is ODD May I again use the Restraint on Water During NPT Equilibration ? or May I continue the MD ? Thanks Advance -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Potential energy from a previous configuration mismatch
On 11/29/12 9:59 AM, juan-manuel.casti...@mv.uni-kl.de wrote: Dear Gromacs friends, I am running some simulations of a hexane/ethanol mixture in a box, using a United-Atom OPLS model. My Gromacs version is the 4.5.5. I fill the simulation box with genbox (I have also used an equilibrated pdb file generated by other simulation code), and I run a energy minimization simulation, wich gives the following energies for the final configuration: Energies (kJ/mol) Angle Fourier Dih. LJ-14Coulomb-14LJ (SR) 6.62915e+005.17493e+02 -2.61388e+01 0.0e+00 -4.01422e+03 Disper. corr. Coulomb (SR) RF excl. Potential Pres. DC (bar) -9.65799e+010.0e+000.0e+00 -3.61282e+030.0e+00 Potential Energy = -3.6128213e+03 Maximum force = 2.7169607e+01 on atom 541 Norm of force = 3.9986315e+00 I take the final configuration, and using exactly the same force field definition and simulation parameters (cutoff radious, electrostatic method, etc), I start a molecular dynamics simulation in the NVE ensemble. No matter what I do, I always have a blow-up problem. I have checked all the points that could be giving the problem, in particular the ones given here: http://www.gromacs.org/Documentation/Terminology/Blowing_Up and I have also tried to modify one by one different parameters, but I never succeed to obtain a running simulation. I have seen that I always have a much larger energy at the beginning of the simulation than the energy at the end of the minimization: Energies (kJ/mol) Angle Fourier Dih. LJ-14Coulomb-14LJ (SR) 5.43743e+042.06120e+036.02532e+01 0.0e+001.62817e+07 Disper. corr. Coulomb (SR) RF excl. PotentialKinetic En. -9.65799e+010.0e+000.0e+00 1.63381e+071.65906e+10 Total EnergyTemperature Pres. DC (bar) Pressure (bar) Constr. rmsd 1.66069e+10 but the potential energy should be exactly the same in both cases, as it only depends on the atomic positions. Anybody can tell me what I am doing wrong? Can you post a complete .mdp file? In theory, if one evaluates the same configuration under the same parameters (i.e. in a single-point energy evaluation), yes, the energies reported should be the same. But doing EM and doing MD are not the same, especially if you are introducing constraints or other parameters. -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] About Diffusion of Water towards Protein in ceter of box
On 11/29/12 10:09 AM, vidhya sankar wrote: Dear Justin, Thank you for your Previous Reply To avoid the Diffusion of Water You Suggested me s follows The better approach would be a position restrain along the z-axis only, allowing the lipids to perhaps re-orient and pack a bit better, followed by NVT equilibration in the absence of any restraints on water. According to your Suggestion Should i Do the Two times Equilibration With restraint On water only in First NVT equilibration followed by another NVT equilibration without restraint on Water But Only With Lipids ? In what way would you restrain the lipids? I could see some value to an initial z-dimension restraint, but ultimately you're going to want to allow both the lipids and water to move freely, otherwise you're not equilibrating very well, you're inhibiting the process. My Question is Can i simultaneously use Restraint for water and Lipids in Single NVT equilibration ? Sure, if done carefully. If i can My NVT equilibration is Successful (means No Diffusion of Water in the Tail Part.) But After That When I do NPT Equilibration There is Diffusion Of Some Water molecules Towards the protein in the center of box Not towards Tail of Lipids Is this Behavior is ODD or Normal ? If it is ODD May I again use the Restraint on Water During NPT Equilibration ? or May I continue the MD ? I have no idea what this means. -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] segmentation fault
Sir, I have one more doubt. During NVT equilibration mdrun giving segmentation fault and not generating any gro files and generating two pdb files. The message is like this Wrote pdb files with previous and current coordinates Warning: 1-4 interaction between 485 and 490 at distance 3.874 which is larger than the 1-4 table size 2.200 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size Segmentation fault why this fault?plz give a solution to overcome it. -- 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] segmentation fault
On 11/29/12 10:44 AM, Shine A wrote: Sir, I have one more doubt. During NVT equilibration mdrun giving segmentation fault and not generating any gro files and generating two pdb files. The message is like this Wrote pdb files with previous and current coordinates Warning: 1-4 interaction between 485 and 490 at distance 3.874 which is larger than the 1-4 table size 2.200 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size Segmentation fault why this fault?plz give a solution to overcome it. http://www.gromacs.org/Documentation/Terminology/Blowing_Up -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] Does GPU support ATI card?
hello: I am just wondering does Gromacs GPU accerlation suppport ATI card? THX Albert -- 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] Does GPU support ATI card?
No. -- Szilárd On Thu, Nov 29, 2012 at 5:15 PM, Albert mailmd2...@gmail.com wrote: hello: I am just wondering does Gromacs GPU accerlation suppport ATI card? THX Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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] Computing energies using g_energy (is -nmol mandatory?)
Hello all, I am trying to compute total energies of several systems, but I am not sure if I am doing it the right way. Until now I simply used the command: g_energy -f file.edr -s file.tpr -o ener.xvg But after reading the manual, I found the -nmol (number of molecules in your sample) flag. If you are comparing systems formed by the same amount of molecules the relative energy is not affected. Still, if I am comparing energies of systems with different compositions this flag will affect them drastically... Is this option mandatory? Thank you very much for your time, Andre -- 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] water mediated hydrogen bond
Hi all, I would like to measure the water mediated hydrogen bond between the ligand and the protein. When I searched the forum I could able to get the link (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/Scripts/plot_hbmap.txt) for the script with which we can get the above mentioned objective. But I'm not sure how to use it Can any one help me with what data I should have before running the script and how I can get such a data and also how shuld I use the data as a input for the script?. Thanks in advance -- View this message in context: http://gromacs.5086.n6.nabble.com/water-mediated-hydrogen-bond-tp5003358.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: Potential energy from a previous configuration mismatch
This is my mdp file for energy minimization: constraints = none ; integration parameters integrator = l-bfgs dt = 0.00 nsteps= 15000 ; center of mass removal nstcomm = 10 comm_mode = Linear ; neighbour searching nstlist = 1 ns_type = grid pbc= xyz rlist= 1.4 ; electrostatics coulombtype = Reaction-Field-zero rcoulomb = 1.1 epsilon_r = 1.0 epsilon_rf = 0.0 ; van der Waals interactions vdwtype = cut-off rvdw = 1.4 DispCorr = EnerPres ; Ewald parameters fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-6 optimize_fft = yes ; energy minimization emtol= 0.1 emstep = 0.01 And this is the one for MD constraints = none ; integration parameters integrator = md tinit = 0 dt = 0.001 nsteps= 1000 ;init_step= 0 comm_mode= linear nstcomm = 10 ; output control nstxout = 1 nstvout = 1 nstfout = 0 nstlog = 1 energygrps= hexane-UA ethanol ; neigbour searching nstlist = 1 ns_type= grid pbc = xyz rlist = 1.4 ; electrostatics coulombtype = Reaction-Field-zero rcoulomb = 1.1 epsilon_r = 1.0 epsilon_rf = 0.0 ; van der Waals interactions vdwtype = cut-off rvdw = 1.4 DispCorr = EnerPres ; Ewald parameters fourierspacing = 0.12 fourier_nx= 0 fourier_ny= 0 fourier_nz= 0 pme_order = 4 ewald_rtol= 1e-6 optimize_fft = yes ; Generate velocities gen_vel = yes gen_temp= 298.0 gen_seed = -1 To use as the starting configuration the last configuration of the minimization, I used the confout.gro file of the minimization as the input conf.gro for MD. I also tried using the traj.trr file generated after minimization with the grompp option -t for MD. I used the same top and ndx files in both simulations. Thanks -- View this message in context: http://gromacs.5086.n6.nabble.com/Potential-energy-from-a-previous-configuration-mismatch-tp5003352p5003359.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] Does GPU support ATI card?
tha't strange, from the link: https://simtk.org/project/xml/downloads.xml?group_id=161 we can see, it said: The current release of OpenMM and OpenMM-accelerated GROMACS enables acceleration of molecular dynamics on specific NVIDIA and ATI GPU cards. I've got ATI-Radeon HD5770, I tried both openMM and withou openMM 4.6, it always claimed couldn't find CUDA device. What's happening? On 11/29/2012 05:44 PM, Szilárd Páll wrote: No. -- Szilárd On Thu, Nov 29, 2012 at 5:15 PM, Albert mailmd2...@gmail.com wrote: hello: I am just wondering does Gromacs GPU accerlation suppport ATI card? THX Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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] Does GPU support ATI card?
Hi Albert, That claim is false. The current mdrun-opnemm version only supports the CUDA OpenMM plugin and even that is not fully supported as we don't have enough resources to maintain the code. We will make sure to get the false claim of ATI GPU support removed from the OpenMM website. Cheers, -- Szilárd PS: we are looking for volunteers to maintain the Gromacs OpenMM integration and in the lack of such people we will have to resort to dropping OpenMM support post-4.6. On Thu, Nov 29, 2012 at 6:36 PM, Albert mailmd2...@gmail.com wrote: tha't strange, from the link: https://simtk.org/project/xml/**downloads.xml?group_id=161https://simtk.org/project/xml/downloads.xml?group_id=161 we can see, it said: The current release of OpenMM and OpenMM-accelerated GROMACS enables acceleration of molecular dynamics on specific NVIDIA and ATI GPU cards. I've got ATI-Radeon HD5770, I tried both openMM and withou openMM 4.6, it always claimed couldn't find CUDA device. What's happening? On 11/29/2012 05:44 PM, Szilárd Páll wrote: No. -- Szilárd On Thu, Nov 29, 2012 at 5:15 PM, Albert mailmd2...@gmail.com wrote: hello: I am just wondering does Gromacs GPU accerlation suppport ATI card? THX Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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] Does GPU support ATI card?
On 11/29/2012 06:44 PM, Szilárd Páll wrote: Hi Albert, That claim is false. The current mdrun-opnemm version only supports the CUDA OpenMM plugin and even that is not fully supported as we don't have enough resources to maintain the code. We will make sure to get the false claim of ATI GPU support removed from the OpenMM website. Cheers, -- Szilárd PS: we are looking for volunteers to maintain the Gromacs OpenMM integration and in the lack of such people we will have to resort to dropping OpenMM support post-4.6. Hello Szilard: thanks for kind comments. If there are not so much people use openMM, probably you can consider give it up. Currently I am using NVIDIA GTX590 GPU acceleration with Gromacs4.6 without openMM support, and it works fine (I did some tests comparing with CPU running results for my system). If I were you, I will save my time and energy focus on current version and road. I am asking if it support ATI just because I've got a stupid MAC Pro machine these days, and it claimed to have a very good ATI GPU, so I just wondering if it could support ATI GPU accelerations. It since that, almost all MD tools only support NVIDIA GPU. best Albert -- 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] Does GPU support ATI card?
On 11/29/12 12:51 PM, Albert wrote: On 11/29/2012 06:44 PM, Szilárd Páll wrote: Hi Albert, That claim is false. The current mdrun-opnemm version only supports the CUDA OpenMM plugin and even that is not fully supported as we don't have enough resources to maintain the code. We will make sure to get the false claim of ATI GPU support removed from the OpenMM website. Cheers, -- Szilárd PS: we are looking for volunteers to maintain the Gromacs OpenMM integration and in the lack of such people we will have to resort to dropping OpenMM support post-4.6. Hello Szilard: thanks for kind comments. If there are not so much people use openMM, probably you can consider give it up. Currently I am using NVIDIA GTX590 GPU acceleration with Gromacs4.6 without openMM support, and it works fine (I did some tests comparing with CPU running results for my system). If I were you, I will save my time and energy focus on current version and road. This would be very unfortunate, I think, but I understand the need to focus on the most feasible development, using the time people have to commit to it, and perhaps priorities are elsewhere. We invested heavily in a few GPU workstations in recent years with the intent of doing a lot of GPU-enabled implicit solvent simulations. Without the GPU, the implicit solvent code is severely limited without fixes to the parallelization on CPU. It seems that the same issues (i.e. one cannot use more than 2 processors for a run) still persist thus far in the development of 4.6, with the focus of using GPU's in a more generalized way, but without OpenMM, implicit solvent simulations (in my hands at least) are not worth it. Of course, running explicit-solvent simulations on GPU is quite nice, but still, the point stands that the implicit code is rendered largely obsolete without GPU. -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] water mediated hydrogen bond
On 11/29/12 10:18 AM, Raj wrote: Hi all, I would like to measure the water mediated hydrogen bond between the ligand and the protein. When I searched the forum I could able to get the link (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/Scripts/plot_hbmap.txt) for the script with which we can get the above mentioned objective. But I'm not sure how to use it Can any one help me with what data I should have before running the script and how I can get such a data and also how shuld I use the data as a input for the script?. Thanks in advance My script will tell you how long a particular hydrogen bond persists, in terms of the percentage of time occupied in a given trajectory. Likely what I suggested was to use the same logic to parse an hbmap.xpm file to determine when hydrogen bonds existed simultaneously between different proteins and a common water molecule. One could, in theory, expand the script I wrote to do this. Having never had a need to make such modifications, I cannot provide much more insight, but I know it is possible. -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] Computing energies using g_energy (is -nmol mandatory?)
On 11/29/12 11:53 AM, André Ferreira wrote: Hello all, I am trying to compute total energies of several systems, but I am not sure if I am doing it the right way. Until now I simply used the command: g_energy -f file.edr -s file.tpr -o ener.xvg But after reading the manual, I found the -nmol (number of molecules in your sample) flag. If you are comparing systems formed by the same amount of molecules the relative energy is not affected. Still, if I am comparing energies of systems with different compositions this flag will affect them drastically... Is this option mandatory? I suppose it depends on what your systems are and what you are trying to measure. The -nmol flag will simply divide the energy values by this value, which is useful for certain metrics in homogeneous systems. By default, the total energy printed is in kJ/(mol of equivalent systems). It wouldn't make sense, for instance, in a membrane-protein system that includes water, since there are several types of distinct molecules there. The statement you always need to set the number of molecules with -nmol only refers to the properties shown in that table in the manual/help description. -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] query regarding PMF calculation
On 11/29/12 11:55 AM, Timir Hajari wrote: Hi, I am trying to calculate PMF using pull code by freezing two pull groups as I need to calculate PMF for a particular orientation. Is it meaning to use pull code in this condition(freezing two pull groups) ?? I will wait for your helpful suggestions. I don't see what the purpose is. If the two molecules are frozen, there is no point in applying a restraint potential between them, since their positions are (by definition) invariant based on the application of freezing. -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: Отв: [gmx-users] Hbonds between Adenine and Thymine
On 11/29/12 2:04 PM, Hovakim Grabski wrote: Dear Justin, I only used pdb2gmx when I prepared the DNA which I created with nab. and the command that I used was: make_ndx -f md_0_1.gro -o index.ndx after that then I press r10 and r17 I get : 14 r_10:64 atoms 15 r_17:64 atoms This are the coordinates for the residues: First strand: 10DA P 281 16.129 2.602 11.551 -0.0064 -0.0090 -0.0438 10DA O1P 282 16.266 2.580 11.500 -0.1992 -0.7975 -0.2387 10DA O2P 283 16.071 2.493 11.632 -0.2097 0.0667 -0.0880 10DA O5' 284 16.120 2.736 11.641 -0.2017 -0.2302 0.2683 10DA C5' 285 16.192 2.847 11.592 -0.0631 -0.2091 0.5162 10DAH5'1 286 16.168 2.856 11.486 0.2017 0.7446 0.5318 10DAH5'2 287 16.299 2.837 11.607 0.0847 2.3049 1.7097 10DA C4' 288 16.169 2.980 11.662 0.0289 -0.3183 0.7520 10DA H4' 289 16.224 3.053 11.601 -2.8707 0.5718 -0.9869 10DA O4' 290 16.034 3.020 11.656 0.3066 0.6132 0.4536 10DA C1' 291 15.987 3.045 11.787 -0.2499 0.3562 0.3063 10DA H1' 292 15.998 3.152 11.802 -0.0905 0.4135 -0.2041 10DA N9 293 15.847 3.001 11.796 -0.1361 0.0295 0.4799 10DA C8 294 15.791 2.875 11.795 -0.1763 0.0476 -0.2015 10DA H8 295 15.862 2.793 11.796 -0.2033 0.0265 0.2737 10DA N7 296 15.664 2.871 11.823 -0.1286 0.2671 0.0604 10DA C5 297 15.619 3.001 11.805 -0.4228 0.2070 0.3483 10DA C6 298 15.497 3.069 11.794 -0.3949 0.2036 -0.0034 10DA N6 299 15.374 3.018 11.804 -0.2308 -0.1144 0.4274 10DA H61 300 15.305 3.085 11.771 1.7600 0.9756 -1.8289 10DA H62 301 15.354 2.923 11.833 -0.2605 -0.3058 -0.1869 10DA N1 302 15.497 3.202 11.778 0.3602 0.1422 -0.5486 10DA C2 303 15.612 3.265 11.760 0.0189 0.7232 -0.7343 10DA H2 304 15.626 3.372 11.756 3.6933 0.5922 2.5222 10DA N3 305 15.732 3.208 11.755 -0.4260 -0.2664 -0.3708 10DA C4 306 15.732 3.076 11.784 -0.2117 -0.1027 0.3843 10DA C3' 307 16.212 2.987 11.809 0.1076 0.4852 0.7002 10DA H3' 308 16.269 2.895 11.822 -0.9751 -0.4630 -0.7702 10DA C2' 309 16.078 2.963 11.878 -0.1301 0.3788 0.2079 10DAH2'1 310 16.053 2.856 11.876 -0.9477 0.5118 1.5833 10DAH2'2 311 16.071 3.003 11.979 0.2289 0.9076 0.0218 10DA O3' 312 16.289 3.101 11.839 0.7852 0.0886 0.4921 17DT P 505 14.540 2.457 13.806 -0.1135 -0.3293 0.2579 17DT O1P 506 14.515 2.332 13.730 -0.3178 -0.1552 0.0391 17DT O2P 507 14.426 2.509 13.885 -0.5793 -0.3100 -0.4187 17DT O5' 508 14.667 2.425 13.901 -0.0420 -0.1432 0.2251 17DT C5' 509 14.775 2.352 13.848 -0.0056 0.1138 -0.0585 17DTH5'1 510 14.807 2.394 13.753 -0.0386 0.1388 -0.0585 17DTH5'2 511 14.747 2.249 13.827 2.0093 -0.8479 1.6171 17DT C4' 512 14.889 2.350 13.950 0.3616 0.2283 -0.4642 17DT H4' 513 14.975 2.306 13.899 1.2315 0.1760 0.9966 17DT O4' 514 14.921 2.483 13.982 0.5698 0.0309 0.1646 17DT C1' 515 14.968 2.485 14.115 0.1427 0.4216 0.3154 17DT H1' 516 15.075 2.506 14.109 0.2135 -0.2028 -1.2027 17DT N1 517 14.902 2.590 14.194 -0.3299 0.5140 -0.2027 17DT C6 518 14.766 2.600 14.188 -0.4375 -0.3782 0.5725 17DT H6 519 14.711 2.537 14.119 0.9370 -0.6147 -0.3448 17DT C5 520 14.704 2.694 14.264 -0.2228 0.0885 0.1776 17DT C7 521 14.556 2.708 14.239 -0.0922 0.0466 -0.6345 17DT H71 522 14.520 2.617 14.190 1.5759 -0.4976 -0.9099 17DT H72 523 14.508 2.720 14.336 1.6175 -1.7512 0.5049 17DT H73 524 14.543 2.797 14.177 0.6660 0.4976 -0.1693 17DT C4 525 14.782 2.793 14.333 0.0191 -0.5878 0.8877 17DT O4 526 14.727 2.896 14.373 -0.1581 -0.1795 -0.3746 17DT N3 527 14.918 2.765 14.347 0.1422 -0.1924 0.4985 17DT H3 528 14.971 2.834 14.397 0.3132 0.9994 -1.2291 17DT C2 529 14.983 2.664 14.278 -0.0217 0.1747 -0.2008 17DT O2 530 15.106 2.660 14.287 -0.0771 -0.0313 0.4614 17DT C3' 531 14.859 2.268 14.075 0.3169 0.4173 -0.3515 17DT H3' 532 14.756 2.283 14.109 0.3908 -0.8417 0.4979 17DT C2' 533 14.947 2.345 14.173 0.2886 0.2008 -0.1552 17DTH2'1 534 14.907 2.335 14.274 -0.4318 -1.3965 -0.5681 17DTH2'2 535 15.047 2.302 14.178 0.9026 1.0206 -3.1872 17DT O3' 536 14.903 2.134 14.068 0.1630 0.3529 -0.0944 Second strand: 10DA P 1106 9.991 9.662 5.857 0.2711 -0.2003 -0.2055 10DA O1P 1107 10.117 9.699 5.925 0.0171 -0.1521
Re: [gmx-users] Re: Potential energy from a previous configuration mismatch
On 11/29/12 10:40 AM, escajarro wrote: This is my mdp file for energy minimization: constraints = none ; integration parameters integrator = l-bfgs dt = 0.00 nsteps= 15000 ; center of mass removal nstcomm = 10 comm_mode = Linear ; neighbour searching nstlist = 1 ns_type = grid pbc= xyz rlist= 1.4 ; electrostatics coulombtype = Reaction-Field-zero rcoulomb = 1.1 epsilon_r = 1.0 epsilon_rf = 0.0 ; van der Waals interactions vdwtype = cut-off rvdw = 1.4 DispCorr = EnerPres ; Ewald parameters fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-6 optimize_fft = yes ; energy minimization emtol= 0.1 emstep = 0.01 And this is the one for MD constraints = none ; integration parameters integrator = md tinit = 0 dt = 0.001 nsteps= 1000 ;init_step= 0 comm_mode= linear nstcomm = 10 ; output control nstxout = 1 nstvout = 1 nstfout = 0 nstlog = 1 energygrps= hexane-UA ethanol ; neigbour searching nstlist = 1 ns_type= grid pbc = xyz rlist = 1.4 ; electrostatics coulombtype = Reaction-Field-zero rcoulomb = 1.1 epsilon_r = 1.0 epsilon_rf = 0.0 ; van der Waals interactions vdwtype = cut-off rvdw = 1.4 DispCorr = EnerPres ; Ewald parameters fourierspacing = 0.12 fourier_nx= 0 fourier_ny= 0 fourier_nz= 0 pme_order = 4 ewald_rtol= 1e-6 optimize_fft = yes ; Generate velocities gen_vel = yes gen_temp= 298.0 gen_seed = -1 To use as the starting configuration the last configuration of the minimization, I used the confout.gro file of the minimization as the input conf.gro for MD. I also tried using the traj.trr file generated after minimization with the grompp option -t for MD. I used the same top and ndx files in both simulations. The .mdp files look reasonable enough, though setting nstlist = 1 during MD will cost you a lot of performance. A value in the 5-10 range should suffice. Do other ensembles work, like NVT? Does a smaller timestep affect stability? -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] Does GPU support ATI card?
Hi Justin, First of all, thanks for the feedback. I find in unfortunate that this information got public in the form of a by the way. More official wording should follow. I wish it happened differently, but unfortunately things did not come together as we thought they would. Dragging along code that for the outsider seems supported, but in reality it is not properly maintained is not beneficial to anyone. Therefore, we decided to demote mdrun-openmm from core to contrib feature status. However, as we don't have a maintainer for the code yet, the official state is not fully supported contrib feature -- unless we find someone to help with at least minimal support for 4.6. I don't like to leave behind my own code, but the situation requires us to focus our efforts on other things. The plan is to include native GPU accelerated GB kernels in the next GROMACS release. While there is a good chance that the code itself will become available in a development branch rather soon, you will not be able to use this code in release version before the next release, 5.0. On Thu, Nov 29, 2012 at 7:54 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/29/12 12:51 PM, Albert wrote: On 11/29/2012 06:44 PM, Szilárd Páll wrote: Hi Albert, That claim is false. The current mdrun-opnemm version only supports the CUDA OpenMM plugin and even that is not fully supported as we don't have enough resources to maintain the code. We will make sure to get the false claim of ATI GPU support removed from the OpenMM website. Cheers, -- Szilárd PS: we are looking for volunteers to maintain the Gromacs OpenMM integration and in the lack of such people we will have to resort to dropping OpenMM support post-4.6. Hello Szilard: thanks for kind comments. If there are not so much people use openMM, probably you can consider give it up. Currently I am using NVIDIA GTX590 GPU acceleration with Gromacs4.6 without openMM support, and it works fine (I did some tests comparing with CPU running results for my system). If I were you, I will save my time and energy focus on current version and road. This would be very unfortunate, I think, but I understand the need to focus on the most feasible development, using the time people have to commit to it, and perhaps priorities are elsewhere. We invested heavily in a few GPU workstations in recent years with the intent of doing a lot of GPU-enabled implicit solvent simulations. Without the GPU, the implicit solvent code is severely limited without fixes to the parallelization on CPU. To be honest I am not aware of the limitations you are referring to, nor the current difference between CPU and GPU implicit solvent performance. It seems that the same issues (i.e. one cannot use more than 2 processors for a run) still persist thus far in the development of 4.6, with the focus of using GPU's in a more I'm especially not aware of such a limitation and it sounds more like a bug than a feature. generalized way, but without OpenMM, implicit solvent simulations (in my hands at least) are not worth it. Of course, running explicit-solvent simulations on GPU is quite nice, but still, the point stands that the implicit code is rendered largely obsolete without GPU. As you rely heavily on implicit solvent code in GROMACS, we could use some help from you. First and foremost, could you please report in form of a redmine issue and/or a mail to the dev-list the current issues you are having/you know of with both CPU and GPU implicit solvent code? We can continue the discussion on on those topic then. Cheers, -- Szilárd -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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] Does GPU support ATI card?
On 11/29/12 6:40 PM, Szilárd Páll wrote: Hi Justin, First of all, thanks for the feedback. I find in unfortunate that this information got public in the form of a by the way. More official wording should follow. I wish it happened differently, but unfortunately things did not come together as we thought they would. Dragging along code that for the outsider seems supported, but in reality it is not properly maintained is not beneficial to anyone. Therefore, we decided to demote mdrun-openmm from core to contrib feature status. However, as we don't have a maintainer for the code yet, the official state is not fully supported contrib feature -- unless we find someone to help with at least minimal support for 4.6. I don't like to leave behind my own code, but the situation requires us to focus our efforts on other things. The plan is to include native GPU accelerated GB kernels in the next GROMACS release. While there is a good chance that the code itself will become available in a development branch rather soon, you will not be able to use this code in release version before the next release, 5.0. If there's intent to create native GPU features within Gromacs, I'm totally fine with it. Quality over time is certainly preferred to somewhat functional stuff now. Further comments below... On Thu, Nov 29, 2012 at 7:54 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/29/12 12:51 PM, Albert wrote: On 11/29/2012 06:44 PM, Szilárd Páll wrote: Hi Albert, That claim is false. The current mdrun-opnemm version only supports the CUDA OpenMM plugin and even that is not fully supported as we don't have enough resources to maintain the code. We will make sure to get the false claim of ATI GPU support removed from the OpenMM website. Cheers, -- Szilárd PS: we are looking for volunteers to maintain the Gromacs OpenMM integration and in the lack of such people we will have to resort to dropping OpenMM support post-4.6. Hello Szilard: thanks for kind comments. If there are not so much people use openMM, probably you can consider give it up. Currently I am using NVIDIA GTX590 GPU acceleration with Gromacs4.6 without openMM support, and it works fine (I did some tests comparing with CPU running results for my system). If I were you, I will save my time and energy focus on current version and road. This would be very unfortunate, I think, but I understand the need to focus on the most feasible development, using the time people have to commit to it, and perhaps priorities are elsewhere. We invested heavily in a few GPU workstations in recent years with the intent of doing a lot of GPU-enabled implicit solvent simulations. Without the GPU, the implicit solvent code is severely limited without fixes to the parallelization on CPU. To be honest I am not aware of the limitations you are referring to, nor the current difference between CPU and GPU implicit solvent performance. It seems that the same issues (i.e. one cannot use more than 2 processors for a run) still persist thus far in the development of 4.6, with the focus of using GPU's in a more I'm especially not aware of such a limitation and it sounds more like a bug than a feature. Right, I filed a bug report a long time ago: http://redmine.gromacs.org/issues/777 Berk applied a band-aid such that one can only use 2 processors for running on CPU. In my mind, this remains a bug, but at least it is possible to run. The failures are somehow related to constraints being split over multiple processors, and mdrun quickly exits with a fatal error if one tries to run using more than 2 processors. I can certainly file a new Redmine feature request to make sure we consider a better resolution for the future. generalized way, but without OpenMM, implicit solvent simulations (in my hands at least) are not worth it. Of course, running explicit-solvent simulations on GPU is quite nice, but still, the point stands that the implicit code is rendered largely obsolete without GPU. As you rely heavily on implicit solvent code in GROMACS, we could use some help from you. First and foremost, could you please report in form of a redmine issue and/or a mail to the dev-list the current issues you are having/you know of with both CPU and GPU implicit solvent code? We can continue the discussion on on those topic then. I can certainly do that. I suspect most of the problems (aside from the one described above) are related to OpenMM. A good number of my simulations simply crash for no discernible reason. I reported some a while ago and got no feedback, so I just basically abandoned that approach and have been waiting for the official 4.6 release to run explicit solvent stuff on GPU. In any case, I'm happy to keep following up on such things. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540)
[gmx-users] How are the charges of the gromos96 forcefiel calculated ?
Dear users, I'm trying to find out how the atoms charges in the GROMOS96 force field were calculated but I've not been able to find out in the manual or in the paper I saw so far. I know that the force fields for MM have the atoms charges calculated by ab initio mathods but I wonder with method was used to GROMOS96. Was it B3LYP 6-31G* in the same way as for OPLSaa ? Thanks for helping. Tanos C. C. Franca. -- 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] How are the charges of the gromos96 forcefiel calculated ?
On 11/29/12 9:06 PM, Tanos Franca wrote: Dear users, I'm trying to find out how the atoms charges in the GROMOS96 force field were calculated but I've not been able to find out in the manual or in the paper I saw so far. I know that the force fields for MM have the atoms charges calculated by ab initio mathods but I wonder with method was used to GROMOS96. Was it B3LYP 6-31G* in the same way as for OPLSaa ? The original methodology for Gromos87 and Gromos96 charge derivation is not publicly available, but is in the Gromos software manuals from what I understand. I spoke with a member of their group recently and apparently some basic electron density calculations were done and then charges were fitted empirically until satisfactory results were achieved. We published a paper a few years ago with some suggestions for more definable methodology using common programs: http://pubs.acs.org/doi/abs/10.1021/ci100335w. -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] Build problem with 4.6beta1
Hooray for being the first to report a problem with the beta :) We have a cluster at our university that provides us with access to some CPU-only nodes and some CPU-GPU nodes. I'm having problems with getting 4.6beta1 to build, and I suspect the issue is related to GPU detection. Here are some specifics: FFTW 3.3.3 CMake 2.8.10 gcc 4.3.4 CUDA 4.0 64-bit Linux on AMD hardware GPU nodes have Tesla C2050 cards Commands: cmake ../gromacs-4.6-beta1 -DCMAKE_INSTALL_PREFIX=/home/jalemkul/software/gromacs-46beta1 -DGMX_X11=OFF -DGMX_GPU=ON -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_PREFIX_PATH=/home/jalemkul/software/fftw-3.3.3/ The first step runs alright, but two things to note: 1. It doesn't detect any GPU, which is correct because I'm on a head node and not a compute node: ...-- Looking for NVIDIA GPUs present in the system -- Could not detect NVIDIA GPUs -- Found CUDA: /cm/shared/apps/cuda40/toolkit/4.0.17 (found suitable version 4.0, minimum required is 3.2) ... 2. It says FFTW isn't detected, but it actually is: ... -- checking for module 'fftw3f' -- package 'fftw3f' not found -- Looking for fftwf_plan_r2r_1d in /home/jalemkul/ATHENA/software/fftw-3.3.3/lib/libfftw3f.so -- Looking for fftwf_plan_r2r_1d in /home/jalemkul/ATHENA/software/fftw-3.3.3/lib/libfftw3f.so - found -- Looking for fftwf_have_simd_avx in /home/jalemkul/ATHENA/software/fftw-3.3.3/lib/libfftw3f.so -- Looking for fftwf_have_simd_avx in /home/jalemkul/ATHENA/software/fftw-3.3.3/lib/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /home/jalemkul/ATHENA/software/fftw-3.3.3/lib/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /home/jalemkul/ATHENA/software/fftw-3.3.3/lib/libfftw3f.so - found ... Upon running make, I get an immediate failure: [ 0%] Building NVCC (Device) object src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o nvcc fatal : redefinition of argument 'compiler-bindir' CMake Error at gpu_utils_generated_gpu_utils.cu.o.cmake:206 (message): Error generating /home/jalemkul/gmxbuild/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o make[2]: *** [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/./gpu_utils_generated_gpu_utils.cu.o] Error 1 make[1]: *** [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/all] Error 2 make: *** [all] Error 2 Any ideas? I'm guessing it's related to the GPU detection failing, because I can build on a workstation in our lab that has a C2075 card. -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] Build problem with 4.6beta1
On Thu, Nov 29, 2012 at 9:20 PM, Justin Lemkul jalem...@vt.edu wrote: Hooray for being the first to report a problem with the beta :) We have a cluster at our university that provides us with access to some CPU-only nodes and some CPU-GPU nodes. I'm having problems with getting 4.6beta1 to build, and I suspect the issue is related to GPU detection. Here are some specifics: FFTW 3.3.3 CMake 2.8.10 gcc 4.3.4 CUDA 4.0 64-bit Linux on AMD hardware GPU nodes have Tesla C2050 cards Commands: cmake ../gromacs-4.6-beta1 -DCMAKE_INSTALL_PREFIX=/home/jalemkul/software/gromacs-46beta1 -DGMX_X11=OFF -DGMX_GPU=ON -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_PREFIX_PATH=/home/jalemkul/software/fftw-3.3.3/ The first step runs alright, but two things to note: 1. It doesn't detect any GPU, which is correct because I'm on a head node and not a compute node: ...-- Looking for NVIDIA GPUs present in the system -- Could not detect NVIDIA GPUs This is not a warning just a note. Is this confusing? -- Found CUDA: /cm/shared/apps/cuda40/toolkit/4.0.17 (found suitable version 4.0, minimum required is 3.2) ... 2. It says FFTW isn't detected, but it actually is: ... -- checking for module 'fftw3f' -- package 'fftw3f' not found It checks several ways. The first (pgkconfig) din't work. Again just a note. -- Looking for fftwf_plan_r2r_1d in /home/jalemkul/ATHENA/software/fftw-3.3.3/lib/libfftw3f.so -- Looking for fftwf_plan_r2r_1d in /home/jalemkul/ATHENA/software/fftw-3.3.3/lib/libfftw3f.so - found -- Looking for fftwf_have_simd_avx in /home/jalemkul/ATHENA/software/fftw-3.3.3/lib/libfftw3f.so -- Looking for fftwf_have_simd_avx in /home/jalemkul/ATHENA/software/fftw-3.3.3/lib/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /home/jalemkul/ATHENA/software/fftw-3.3.3/lib/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /home/jalemkul/ATHENA/software/fftw-3.3.3/lib/libfftw3f.so - found ... Upon running make, I get an immediate failure: [ 0%] Building NVCC (Device) object src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o nvcc fatal : redefinition of argument 'compiler-bindir' CMake Error at gpu_utils_generated_gpu_utils.cu.o.cmake:206 (message): Error generating /home/jalemkul/gmxbuild/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o make[2]: *** [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/./gpu_utils_generated_gpu_utils.cu.o] Error 1 make[1]: *** [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/all] Error 2 make: *** [all] Error 2 Any ideas? I'm guessing it's related to the GPU detection failing, because I can build on a workstation in our lab that has a C2075 card. Could be this cmake bug: http://www.gccxml.org/Bug/view.php?id=13674 Could you try whether any other cmake version (e.g. 2.8.9) works? Roland -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 -- 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] Build problem with 4.6beta1
On 11/29/12 9:34 PM, Roland Schulz wrote: On Thu, Nov 29, 2012 at 9:20 PM, Justin Lemkul jalem...@vt.edu wrote: Hooray for being the first to report a problem with the beta :) We have a cluster at our university that provides us with access to some CPU-only nodes and some CPU-GPU nodes. I'm having problems with getting 4.6beta1 to build, and I suspect the issue is related to GPU detection. Here are some specifics: FFTW 3.3.3 CMake 2.8.10 gcc 4.3.4 CUDA 4.0 64-bit Linux on AMD hardware GPU nodes have Tesla C2050 cards Commands: cmake ../gromacs-4.6-beta1 -DCMAKE_INSTALL_PREFIX=/home/jalemkul/software/gromacs-46beta1 -DGMX_X11=OFF -DGMX_GPU=ON -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_PREFIX_PATH=/home/jalemkul/software/fftw-3.3.3/ The first step runs alright, but two things to note: 1. It doesn't detect any GPU, which is correct because I'm on a head node and not a compute node: ...-- Looking for NVIDIA GPUs present in the system -- Could not detect NVIDIA GPUs This is not a warning just a note. Is this confusing? No, it's clear enough, and correct. I just wasn't sure how Gromacs would handle building on a node where there is no GPU, but for which I am requesting a GPU build. I guess it's not related (see below). -- Found CUDA: /cm/shared/apps/cuda40/toolkit/4.0.17 (found suitable version 4.0, minimum required is 3.2) ... 2. It says FFTW isn't detected, but it actually is: ... -- checking for module 'fftw3f' -- package 'fftw3f' not found It checks several ways. The first (pgkconfig) din't work. Again just a note. This one is weirder, but I guess harmless. It's just strange to have the build system say I can't find FFTW, and then say just kidding, it's fine! ;) -- Looking for fftwf_plan_r2r_1d in /home/jalemkul/ATHENA/software/fftw-3.3.3/lib/libfftw3f.so -- Looking for fftwf_plan_r2r_1d in /home/jalemkul/ATHENA/software/fftw-3.3.3/lib/libfftw3f.so - found -- Looking for fftwf_have_simd_avx in /home/jalemkul/ATHENA/software/fftw-3.3.3/lib/libfftw3f.so -- Looking for fftwf_have_simd_avx in /home/jalemkul/ATHENA/software/fftw-3.3.3/lib/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /home/jalemkul/ATHENA/software/fftw-3.3.3/lib/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /home/jalemkul/ATHENA/software/fftw-3.3.3/lib/libfftw3f.so - found ... Upon running make, I get an immediate failure: [ 0%] Building NVCC (Device) object src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o nvcc fatal : redefinition of argument 'compiler-bindir' CMake Error at gpu_utils_generated_gpu_utils.cu.o.cmake:206 (message): Error generating /home/jalemkul/gmxbuild/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o make[2]: *** [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/./gpu_utils_generated_gpu_utils.cu.o] Error 1 make[1]: *** [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/all] Error 2 make: *** [all] Error 2 Any ideas? I'm guessing it's related to the GPU detection failing, because I can build on a workstation in our lab that has a C2075 card. Could be this cmake bug: http://www.gccxml.org/Bug/view.php?id=13674 Could you try whether any other cmake version (e.g. 2.8.9) works? Yep, CMake bug. Our previous version was 2.8.3, and that one works fine. I'll install 2.8.9 for future builds. Thanks, Roland. -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] Build problem with 4.6beta1
On Fri, Nov 30, 2012 at 3:20 AM, Justin Lemkul jalem...@vt.edu wrote: Hooray for being the first to report a problem with the beta :) We have a cluster at our university that provides us with access to some CPU-only nodes and some CPU-GPU nodes. I'm having problems with getting 4.6beta1 to build, and I suspect the issue is related to GPU detection. Here are some specifics: FFTW 3.3.3 CMake 2.8.10 gcc 4.3.4 CUDA 4.0 64-bit Linux on AMD hardware GPU nodes have Tesla C2050 cards Note that on AMD you might have to use less threads per process than the default and therefore more than one process per GPU: set -gpu_id=00 for two processes in a node to both use the first GPU. Additionally, you might want to use a newer gcc and CUDA, both will provide performance improvements. Commands: cmake ../gromacs-4.6-beta1 -DCMAKE_INSTALL_PREFIX=/home/** jalemkul/software/gromacs-**46beta1 -DGMX_X11=OFF -DGMX_GPU=ON -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_PREFIX_PATH=/home/ **jalemkul/software/fftw-3.3.3/ The first step runs alright, but two things to note: 1. It doesn't detect any GPU, which is correct because I'm on a head node and not a compute node: ...-- Looking for NVIDIA GPUs present in the system -- Could not detect NVIDIA GPUs -- Found CUDA: /cm/shared/apps/cuda40/**toolkit/4.0.17 (found suitable version 4.0, minimum required is 3.2) ... That is just an informative message. We try to detect GPUs on the build machine to suggest users compiling with GPU acceleration enabled. 2. It says FFTW isn't detected, but it actually is: ... -- checking for module 'fftw3f' -- package 'fftw3f' not found -- Looking for fftwf_plan_r2r_1d in /home/jalemkul/ATHENA/** software/fftw-3.3.3/lib/**libfftw3f.so -- Looking for fftwf_plan_r2r_1d in /home/jalemkul/ATHENA/** software/fftw-3.3.3/lib/**libfftw3f.so - found -- Looking for fftwf_have_simd_avx in /home/jalemkul/ATHENA/** software/fftw-3.3.3/lib/**libfftw3f.so -- Looking for fftwf_have_simd_avx in /home/jalemkul/ATHENA/** software/fftw-3.3.3/lib/**libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /home/jalemkul/ATHENA/** software/fftw-3.3.3/lib/**libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /home/jalemkul/ATHENA/** software/fftw-3.3.3/lib/**libfftw3f.so - found ... Upon running make, I get an immediate failure: [ 0%] Building NVCC (Device) object src/gmxlib/gpu_utils/** CMakeFiles/gpu_utils.dir//./**gpu_utils_generated_gpu_utils.**cu.o nvcc fatal : redefinition of argument 'compiler-bindir' CMake Error at gpu_utils_generated_gpu_utils.**cu.o.cmake:206 (message): Error generating /home/jalemkul/gmxbuild/src/**gmxlib/gpu_utils/CMakeFiles/** gpu_utils.dir//./gpu_utils_**generated_gpu_utils.cu.o make[2]: *** [src/gmxlib/gpu_utils/**CMakeFiles/gpu_utils.dir/./** gpu_utils_generated_gpu_utils.**cu.o] Error 1 make[1]: *** [src/gmxlib/gpu_utils/**CMakeFiles/gpu_utils.dir/all] Error 2 make: *** [all] Error 2 That's bad and I don't exactly know why does it happen, it looks like the nvcc host compiler gets double-set. Could you put your CMakeCache.txt of this configuration into pastbin and link it (attachments are blocked, I think)? One option to get it work is to remove the -ccbin=/path/to/your/gcc form the CUDA_NVCC_FLAGS cache variable and re-configure. -- Szilárd Any ideas? I'm guessing it's related to the GPU detection failing, because I can build on a workstation in our lab that has a C2075 card. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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
