[gmx-users] Metal Ion Position
Hi, I have a question on how to calculate the metal ion position in a protein in a simulation. To be more more specific, I would like to make sure the metal ion stay in the binding site throughout the simulation, and not sure which analysis function to use. I have tried g_rms, and did not work. I'd appreciate your help. Thanks for your help in advance. Simon-- 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] pdb2gmx
Hi, I have a question about pdb2gmx. If a pdb file contains a multiple structures, will it average the coordinates or just pick one of the structures to convert? Thanks for your insight. Simon -- 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] The RMSD of a metal ion
Hi, I would like to look at the positions of a metal ion in MD relative to its original crystal position. I tried g_rms, and I got the following message: Fatal error : Need = 3 points to fit Did I use the correct command to achieve this task? Thanks for your insight in advance. Simon -- 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] g_hbond
Hi, I am little confused about setting up the two groups in g_hbond. 1. Are the two groups corresponding to the donor (N) and the acceptor (O) atoms? I want to measure the lifetime, angle and distance of the triplet N-HO hydrogen bond. Is this the triplet that the manual talks about? Thanks for your insight. Simon -- 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] g_hbond
Hi, To help clarify my previous g_hbond question, I have these two groups in my index file [ a_100_a_101] # 100 is N, #101 is H 100 101 [ a_200 ] # 200 is O 200 when I ran g_hbond, I got Found 1 donors and 2 acceptors. The part that I don't quite understand is why it says 2 acceptors. Did I set up the groups correctly? Again, hope this clarifies my question. Thanks for your insight. Simon -- 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] CHARMM forcefield
Hi, I have two questions about using the charmm force field. 1. Do we still need to use the two perl scripts, convert_charmm_ to_gromacs.pl and fix_top_for_charmm.pl? 2. I got the following note when I tried to do energy minim. with grompp: NOTE 1 [file topol.top]: The largest charge group contains 12 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. Is this a problem? Thanks for your insight! Simon -- 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] g_rotacf
Hi, I have tried to use g_rotacf to get the rotational autocorrelation plot for a n-h vector, and I have two questions: 1. My MD run is 20ns, but the rotacf.xvg shows only 10ns. why? 2. The plot is bottom out at 500 ps and then go back up. What does it mean physically? Thanks for your insight. Simon -- 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] oplsaa vs. charmm
Hi, I have recently done two simulations on a protein at high temperature near its melting temperature. At the beginning I used CHARMM forcefield, and then OPLSAA to double check the results. There are some differences in the structures between the forcefield used. I know different forcefields can give different results. All parameters in the simulations were the same except the forcefield. Is there anyway I can tell which forcefield gives more reliable results? Thanks for the insights, Simon -- 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] oplsaa vs. charmm
Hi, Once again, I appreciate all the responses. 1. To correct I just had in the previous email. I used GROMOS53ab not CHARMM. My apology. 2. At high temperaure, one of the helical turn in a alpha helix (3 residues) turns into a coil in GROMOS forcefield throughout the 20ns simulation. It was only slightly distorted in OPLSAA simulation in 20ns. 3. The RMSF (backbone) for those 3 residues: 0.3nm in GROMOS vs. 0.1 nm in OPLSAA. As I mentioned, the protein is near its melting temperature, therefore, I am not surprised to see some helix to coil transition or helical distortions. As Justin has suggested, I probably will try to make a longer run to see what will happen. Best, Simon --- On Fri, 5/27/11, Peter C. Lai p...@uab.edu wrote: From: Peter C. Lai p...@uab.edu Subject: Re: [gmx-users] oplsaa vs. charmm To: simon sham ssha...@yahoo.com Cc: gmx-users@gromacs.org gmx-users@gromacs.org Date: Friday, May 27, 2011, 9:05 AM On 2011-05-27 10:50:14AM -0500, simon sham wrote: Hi, I have recently done two simulations on a protein at high temperature near its melting temperature. At the beginning I used CHARMM forcefield, and then OPLSAA to double check the results. There are some differences in the structures between the forcefield used. I know different forcefields can give different results. All parameters in the simulations were the same except the forcefield. Is there anyway I can tell which forcefield gives more reliable results? Also you never stated what RMSD/RMSFs between the two and if they are significant to what you care to see (i.e. if you expect, say, alpha helix to random coil transition, what changes in the unfolding do you see that make you suspect one forcefield is better than the other?). Also if this is in a solvated system, the rest of the forcefield has been parameterized with the implicit assumption that TIPS3P (Charmm-specific) water will be used so make sure you have switched your water type when using CHARMM. -- == Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | BEC 257 Genetics, Div. of Research | 1150 10th Avenue South p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- 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] g_helix and g_rotacf
Hi, I have two questions about using g-helix and g_rotacf On g_helix, 1. I have used the following command: g_helix -s md.tpr -f md.xtc -n index.ndx -b 1 -e 2 In the index file, I have residues 10-20 as my group. However, when I ran the above command, I did not have the n-ahx.xvg file. Did I miss something here? On g_rotacf, I have used the following commands to calculate the order parameters: trjconv -s md.tpr -f noPBC.xtc -o fit.xtc -fit rot+trans to remove the rotational and translational motion of my protein. g_rotacf -s md.tpr -f fit.xtc -d -n nh - P 2 . In the index file, it lists all the NH pairs except the N atoms from proline. It gave order.xvg and rotacf.xvg. In terms of getting the correct order parameters for each NH, are the above 2 commands correct? Finally, in the manual, it mentions about the triplet, i, j, k. What is the meaning of the triplet? Thanks for your insights! Simon -- 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] Rg
Hi, I have a question of using Radius of Gyration to analyze my simulation data for a protein at a temperature that it would unfold. My understanding is that when a protein in an unfolded state, it still have some structure and is not a random coil. So, my question is: Will the Rg value for a unfolded protein be completely different from that of folded one? Thanks for your insight in advance. Simon -- 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] Helix to coil
Hi, Does anyone know the time scale for helical to random coil transition? I have done one simulation and noticed that one helical turn of a helix in the crystal structure becomes a loop in the simulation. Have anyone seen something like this before? Best, Simon -- 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] X-ray Structures
Hi, I have a question about using X-ray PDB files for simulations: 1. Is there any rule of thumb on how good a resolution is required for simulations? I know it has nothing to do with GROMACS. Thanks for your insight. Simon -- 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] g_saltbr
Hi, I am curious how the donor and acceptor atoms are picked with g_saltbr. For examples, with Asp, it picked CG instead of the two ODs, and with LYS, it picked CE instead of NZ. Why? Thanks for your help in advance. Simon Sham -- 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] g_cluster warning message
Hi, I have been trying to generate a pdb file using g_cluster with the following command: g_cluster -s md.tpr -f md.xtc -cl It ran O.K. but I am curious the rmsd warning message: The RMSD ranges from 0.0481586 to 0.200779 nm Average RMSD is 0.124039 Number of structures for matrix 5001 Energy of the matrix is 204.264 nm WARNING: rmsd minimum 0 is below lowest rmsd value 0.0481586 Linking structures ** Sorting and renumbering clusters What is that rmsd minimum 0 all about? Thanks for your help in advance. Simon Sham -- 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] g_chi
Hi, I have 2 questions on using g_chi to calculate only one omega angle for X-Pro. 1. I used the following command: g_chi -s md.gro/tpr -f md.xtc -omega -o test.xvg and got the following message: Fatal error: Library file in current dir nor not found aminoacids.datin default directories. (You can set the directories to search with the GMXLIB path variable) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors; 2. The command does not allow using index file. How can I calculate just one dihedral angle? Thanks for your help in advance. Simon Sham -- 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] g_chi
Hi, Thanks for those who replied my previous questions on g_chi. I just installed the latest version of gromacs 4.5.4 and could run the command. I still have a question about the command: Again, I used the following command: g_chi -s md.tpr -f md.xtc -omega It generated a series of xmgrace files for each residue, but it does not give a residue #. In the chi.log file, it only listed the four omega atom numbers for each residue...that's it. Again thanks for your help in advance. Simon Sham -- 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] g_energy -ravg option
Hi, I need to calculate a running average on pressure, and have problem in using the -ravg option in g_energy command: I have tried the followings: 1. g_energy -f file.edr -ravg ravg.xvg -o pressure.xvg 2. g_energy -f file.edr -ravg -o pressure.xvg I could get the fluctuations in pressure.xvg, but not the running averages. Any help is appreciated in advance. Simon Sham -- 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] SO4
Hi, I posted this question about SO42- in GROMACS two months ago, but I would like to double-check to confirm my MD results: 1. I used gromos53a6.ff force forced for SO42- ion. I have 4 SO4 ions in the original pdb file. 2. When I changed the name SO4 to SO42- in the pdb file as shown in the following line, HETATM 1005 S SO42- A 401 23.925 -3.428 6.383 1.00 35.88 S HETATM 1006 O1 SO42- A 401 24.709 -4.359 7.275 1.00 37.19 OM HETATM 1007 O2 SO42- A 401 23.433 -4.282 5.270 1.00 37.40 OM HETATM 1008 O3 SO42- A 401 22.736 -2.914 7.160 1.00 36.74 OM HETATM 1009 O4 SO42- A 401 24.780 -2.306 5.947 1.00 37.08 OM HETATM 1010 S SO42- A 402 22.214 15.738 8.260 1.00 39.60 S HETATM 1011 O1 SO42- A 402 21.149 15.021 9.051 1.00 39.06 OM HETATM 1012 O2 SO42- A 402 23.462 14.907 7.944 1.00 38.26 OM HETATM 1013 O3 SO42- A 402 21.685 16.282 6.925 1.00 39.20 OM HETATM 1014 O4 SO42- A 402 22.706 16.910 9.124 1.00 39.69 OM HETATM 1015 S SO42- A 403 34.187 9.439 32.376 1.00 60.41 S HETATM 1016 O1 SO42- A 403 35.007 9.343 31.107 1.00 60.53 OM HETATM 1017 O2 SO42- A 403 34.378 8.317 33.355 1.00 60.26 OM HETATM 1018 O3 SO42- A 403 34.624 10.704 33.093 1.00 60.93 OM HETATM 1019 O4 SO42- A 403 32.736 9.578 31.991 1.00 60.64 OM and ran pdb2gmx, instead of having 4 SO42- ions, I only got 1 SO42- ion in the .gro file as follows: 0SO42 S 1235 2.390 2.500 2.800 0SO42 O1 1236 2.470 0.900 5.900 0SO42 O2 1237 2.340 3.300 8.200 0SO42 O3 1238 2.270 3.600 1.400 0SO42 O4 1239 2.470 8.000 0.600 And these coordinates are wrong!! 3. However, when I used SO42 in the pdb file, and ran pdb2gmx, I got all the 4 SO42 coordinates, and they are good, but the program gave the following warnings for the SO42 topology: WARNING: 'SO42' not found in residue topology database, trying to use 'SO42-' FYI, I use 4.5.1 version. Did I do something wrong in the pdb file? Can I ignore the warning message in #3? Thanks for you help in advance, Simon Sham -- 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] g_rmsf
Hi, I am just curious that in the MD community whether there is consensus on how to compare calculated rmsfs and expermental b-factors in x-ray. Should we use average value per residue or one particular atom in a residue for comparsion. Secondly, in NMR, people minimize a number of final calculated structures with energy minimization. Do people do the same thing when they average their structures within a certain time period with g_rmsf or g-covar. Thanks for your insight. Simon Sham -- 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] 2 Questions
Hi, I) I have been trying to figure out where is the source of the following warning message coming from: WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. 2). I used ngmx to inspect the trajectory of a 20ns MD run, and I noticed that the protein is moving around quite a bit in different directions. Is it normal? Thanks for your insight. Simon -- 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] SO4 ion
Hi, I have a crystal structure with several SO4 ions. According to the online manual, the source is ffgmx.rtp. But I could not find it in /gromacs/share/top directory. I also could not find it in several force field files. Just curious how people have treated this ion in their simulations. Thanks for your help. Simon Sham -- 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] Advanced Simulation Analysis
Hi, I have been trying to follow the tutorial posted by David van der Spoel to generate the order parameters at: https://extras.csc.fi/chem/courses/gmx2007/analysis/index.html When I ran g_rotacf, I got the following message: Fatal error: Number of index elements not multiple of 2, these can not be atom doublet. Has anyone tried that tutorial? Best, Simon Sham -- 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 Messages
Hi, I run GROMACS in parallel mode. The first two jobs that I submitted are still running. However, when I tried to submit the third job, and stopped for the following reason: Fatal error: There is no domain decomposition for 10 nodes that is compatible with the given box and a minimum cell size of 1.025 nm Change the number of nodes or mdrun option -rcon or -dds or your LINCS settings Look in the log file for details on the domain decomposition What does the error message mean? Thanks for your help. Best, Simon Sham -- 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] High Temperature simulations
Hi, Is it possible to run simulations at high temperatures? Is there any concern in dealing with the solvent water molecules when running high temperature simulations? Best, Simon Sham -- 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] Protein in a solvated box
Hi, I have protein in a solvated box. When I used VMD to look at the system, I've found that the protein is not located at the center, but rather at the corner section. I would like to know why. Thanks for your insight in advance. Simon -- 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] Missing Amino Acids
Hi, 1. I have a protein which is missing both the first and last amino acids in the sequence. Do you know any free linux softwares that can insert these missing amino acids? 2. Since only two amino acids are missing, one in both end, can I simply ignore them in simulations? Thanks for your insight in advance. Best, Simon -- 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: MPI and dual-core laptop
Hi, I was finally able to get my MPI GROMACS running on my laptop. Thanks for all those who have provided invaluable suggestions. Best, Simon Sham --- On Mon, 9/27/10, simon sham ssha...@yahoo.com wrote: From: simon sham ssha...@yahoo.com Subject: MPI and dual-core laptop To: gmx-users@gromacs.org Date: Monday, September 27, 2010, 11:42 AM Hi, I wanted to test the GROMACS MPI version in my dual-processors laptop. I have installed openmpi 1.4.2 version. However, when I tried to configure GROMACS 4.5.1 with --enable-mpi option, I got the following configuration problem: checking whether the MPI cc command works... configure: error: Cannot compile and link MPI code with mpicc mpicc is in my /usr/local/bin directory. Questions: 1. Can I run GROMACS 4.5.1 in a dual-processor laptop? 2. If yes, how should I configure the software? Thanks in advance for your insight. Best, Simon Sham -- 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] MPI and dual-core laptop
Hi, I wanted to test the GROMACS MPI version in my dual-processors laptop. I have installed openmpi 1.4.2 version. However, when I tried to configure GROMACS 4.5.1 with --enable-mpi option, I got the following configuration problem: checking whether the MPI cc command works... configure: error: Cannot compile and link MPI code with mpicc mpicc is in my /usr/local/bin directory. Questions: 1. Can I run GROMACS 4.5.1 in a dual-processor laptop? 2. If yes, how should I configure the software? Thanks in advance for your insight. Best, Simon Sham -- 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] MPI
Hi, This is the same email that I'd sent yesterday but has not got posted? Hi, I have some questions about installation of GROMACS with MPI. Our system administrator has installed the 4.5.1 version in our system. When I tested the software with openmpi/openmpi-1.3.3-gcc/bin/mpirun with mdrun_mpi, I got all sorts of error message such as opt/apps/gromacs/gromacs-4.5.1-mpi/bin/mdrun_mpi: Symbol `ompi_mpi_byte' has different size in shared object, consider re-linking, and many others. My questions: 1. When I prepare my system for simulations, do I have to consistently use *_mpi functions in gromacs_4.5.1_mpi directory? 2. Are there any details that I need to pay attention when I configure the software with openmpi? Thanks for your help in advance. Best, Simon Sham -- 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: MPI
Hi, Our system system administrator configured the software with --MPI option according to the installation instructions. He told me there were lots of warning messages when he did it. My related question is that since there is LAM/MPI out there as well, can GROMACS 4.5 be configured with OPENMPI? Thanks in advance, Simon Sham Hi, This is the same email that I'd sent yesterday but has not got posted? Hi, I have some questions about installation of GROMACS with MPI. Our system administrator has installed the 4.5.1 version in our system. When I tested the software with openmpi/openmpi-1.3.3-gcc/bin/mpirun with mdrun_mpi, I got all sorts of error message such as opt/apps/gromacs/gromacs-4.5.1-mpi/bin/mdrun_mpi: Symbol `ompi_mpi_byte' has different size in shared object, consider re-linking, and many others. My questions: 1. When I prepare my system for simulations, do I have to consistently use *_mpi functions in gromacs_4.5.1_mpi directory? 2. Are there any details that I need to pay attention when I configure the software with openmpi? Thanks for your help in advance. Best, Simon Sham -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100924/2a671694/attachment-0001.html -- Message: 3 Date: Fri, 24 Sep 2010 15:18:27 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] MPI To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4c9cf983.7010...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Guess my reply never hit the list, either, but it's in the archive: http://lists.gromacs.org/pipermail/gmx-users/2010-September/054259.html -Justin simon sham wrote: Hi, This is the same email that I'd sent yesterday but has not got posted? Hi, I have some questions about installation of GROMACS with MPI. Our system administrator has installed the 4.5.1 version in our system. When I tested the software with openmpi/openmpi-1.3.3-gcc/bin/mpirun with mdrun_mpi, I got all sorts of error message such as opt/apps/gromacs/gromacs-4.5.1-mpi/bin/mdrun_mpi: Symbol `ompi_mpi_byte' has different size in shared object, consider re-linking, and many others. My questions: 1. When I prepare my system for simulations, do I have to consistently use *_mpi functions in gromacs_4.5.1_mpi directory? 2. Are there any details that I need to pay attention when I configure the software with openmpi? Thanks for your help in advance. Best, Simon Sham -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] GROMACS 4.5.1 and MPI
Hi, I have some questions about installation of GROMACS with MPI. Our system administrator has installed the 4.5.1 version in our system. When I tested the software with openmpi/openmpi-1.3.3-gcc/bin/mpirun with mdrun_mpi, I got all sorts of error message such as opt/apps/gromacs/gromacs-4.5.1-mpi/bin/mdrun_mpi: Symbol `ompi_mpi_byte' has different size in shared object, consider re-linking, and many others. My questions: 1. When I prepare my system for simulations, do I have to consistently use *_mpi functions in gromacs_4.5.1_mpi directory? 2. Are there any details that I need to pay attention when I configure the software with openmpi? Thanks for your help in advance. Best, Simon -- 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] Adding Ions
Hi, I have tried to add NaCl into my system in the 4.5.1 version to balance the total charge, and used OPLS forcefield. In the topol file file, it has CL- but no NA+. However, when I ran grompp_d, it gave me the following error message: Program grompp_d, VERSION 4.5.1 Source code file: toppush.c, line: 1987 Fatal error: No such moleculetype CL- It did not happen when I used 4.0.7 version. I checked the top.itp file and CL- is defined. Any clue on how to fix it? Best, Simon -- 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: Adding Ions
Hi, I have figured the problem. Can't use NA+/CL- in the latest version, and have to use NA/CL at least in OPLS. Best, Simon -- 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] Langevin Dynamic bd-temp parameter
Hi, I tried to run a md calculation with a bd-temp = 300 line in my file, but it gave a warning: Unknown left-hand 'bd-temp' in a parameter file Did I use the right parameter for setting up the temperature in Langevin Dynamics? Thanks for your help in advance. Simon Sham - You rock. That's why Blockbuster's offering you one month of Blockbuster Total Access, No Cost.___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] FFTW
Hi, I have tried to install GROMACS in my Slackware linux box. I have fftw 3. something installed separatedly. However, when I configured GROMACS, the fft3 headers were found but not the library files. They are located in /usr/local/include and /usr/local/lib respectively. I also tried to configure with ./configure CPPFLAGS=/usr/local/lib. But it still did not work either. Does anyone know how to fix it? Thanks in advance for your help. Dukeman - Yahoo! oneSearch: Finally, mobile search that gives answers, not web links. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
