[gmx-users] Segmentation fault (core dumped)
Dear all I want to study the diffusion coeffcient of CO in water. I have done the energy minimization step and got the problem segmentation fault during Equilibration. I am confused whether my input file has got some error or the error is in the processing machine.I have made the following .mdp file ; ;PREPROCESSING parameters cpp = /lib/cpp define = -DFLEX_SPCE integrator = md dt =.002 nsteps = 2500 nstcomm = 1 ;OUPUT CONTROL parameters. nstxout = 250 nstvout = 1000 nstfout = 0 nstlog = 100 nstenergy = 100 energygrps = system ;NEIGHBOUR SEARCHING parameters. nstlist = 10 ns_type = grid rlist = 1.0 ;ELECTROSTATIC and VdW parameters. rcoulomb= 1.0 rvdw= 1.0 epsilon-r = 1 ;BERENDSEN TEMPERATURE COUPLING is on in two groups Tcoupl = berendsen tc-grps = system tau_t = 0.01 ref_t = 300 ;PRESSURE COUPLING is on Pcoupl = berendsen tau_p = 0.1 compressibility = 4.6e-5 ref_p = 1.0 ;SIMULATED ANNEALING parameters are not specified. ;GENERATE VELOCITIES is on at 300 K. gen_vel = yes; ; generate initially gen_temp= 300 gen_seed= 173259 ;give different values for different trials. ;BONDS parameters pbc = xyz ; 3-D PBC constraints = all-bonds constraint-algorithm = shake unconstrained-start = no The box size is 2.1 nm. I got no information then Segmentation default.It says nothing regarding the input . I will be pleased if you provide me some suggestions. Ishwor Poudyal TU Nepal -- 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: pullx file content with pull_geometry = position
I update the post to say that we tried to make a rerun of the trajectory on our local machine and the output of the pullx.xvg file (created with the option -px of mdrun) is: # This file was created Wed Jun 5 12:15:49 2013 # by the following command: # mdrun -s ../conf10.tpr -rerun ../conf10.xtc -px pullx_conf10.xvg -pf pullf_conf10.xvg -nt 6 -v # # mdrun is part of G R O M A C S: # # Gravel Rubs Often Many Awfully Cauterized Sores # @title Pull COM @xaxis label Time (ps) @yaxis label Position (nm) @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend 0 X @ s1 legend 0 Y @ s2 legend 0 Z @ s3 legend 1 dX @ s4 legend 1 dY @ s5 legend 1 dZ 0. 3.47835 5.10501 11.644 -0.378345 1.13499 1.73604 20. 3.47852 5.12016 11.6554 -0.446518 1.07184 1.69255 40. 3.49803 5.12013 11.6612 -0.350032 1.12387 1.75475 (...) ** The output of the pullx.xvg file is indeed the distance between the two pull groups, but this is very different numbers than the one obtained during the simulation on a cluster (see above post). So the question stand what are the numbers given in the pullx.xvg file created during the original simulation ? -- View this message in context: http://gromacs.5086.x6.nabble.com/pullx-file-content-with-pull-geometry-position-tp5008797p5008850.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] Projection of crystal structure on PCA plot
Hi ALL, I have carried out a simulation of a protein and have carried out PCA on the entire trajectory. I have obtained a 2D projection plot of EV1 on EV2. Now I want to locate the conformation of the crystal structure (with which I started the MD) on this map. How to do this? Can I use g_anaeig -v Prt_MD_Eigenvec.trr -s Prt.tpr -f crystal.pdb -proj 12.xvg -n Prt_CA.ndx -first 1 -last 2 -2d 2dproj.xvg to obtain the crystal structure position? Or do I need to calculate covariance matrix for the crystal str.(I need a set of them in that case) and then use g_anaeig? Thanks a lot in advance. Regards, Anirban -- 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] Snapshot and co-ordinate query
Hi Justin, Thank you so much for the clarification. Kind regards, Ankita On Wed, Jun 5, 2013 at 11:28 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/5/13 3:03 PM, Ankita naithani wrote: Hi, I have two questions. I have performed a simulation on my protein structure and after the simulation, I used trjconv to obtain snapshots after every 10 ns with the following command: trjconv -f md.xtc -s md.tpr -b 1 -e 10001 -o md_10.pdb This command will produce one snapshot. If you're looking to get multiple snapshots, it is easier to combine -skip -sep to write out multiple snapshots in one command. and chose 0 (system) for the group. However, when I see the same structure in PyMol as cartoon representation, I see the protein structure and few of the residues scattered elsewhere of a particular chain, say chain A. I am concerned whether my residues of that particular chain fragmented during simulation or is my way of obtaining snapshots wrong? The molecule isn't fragmented, it's just split across periodic boundaries. trjconv can take care of that too (see trjconv -h). Also, there was another question, I wanted to know how the geometry is preserved in the average structure as computed by gromacs?The average structure calculated during analysis would be the average of all the atomic positions/co-ordinates during the length of simulation. But, I wanted to know how are the bond angles treated for computation of the average structure? Since, we use the structure for further analysis too. Are the bond lengths distorted or they are retained while average is being computed? Also, what are the co-ordinates used for this computation? http://www.gromacs.org/**Documentation/Terminology/**Average_Structurehttp://www.gromacs.org/Documentation/Terminology/Average_Structure -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 -- Ankita Naithani -- 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] Projection of crystal structure on PCA plot
Hi Anirban, The eigenvectors obtained from the simulation are a way of rewriting the coordinates of your structures, not in terms of atoms-XYZ, but as combinations of these. Because they are combinations of atom-positions, they are defined for the selection of atoms used for the calculation. If your crystal structure has the same atoms, which is true if you did not use hydrogen atoms, or modeled parts for the covariance analysis, then you can project that structure onto the eigenvectors determined, in exactly the way you describe in your question. Hope it helps, Tsjerk On Thu, Jun 6, 2013 at 12:06 PM, Anirban reach.anirban.gh...@gmail.comwrote: Hi ALL, I have carried out a simulation of a protein and have carried out PCA on the entire trajectory. I have obtained a 2D projection plot of EV1 on EV2. Now I want to locate the conformation of the crystal structure (with which I started the MD) on this map. How to do this? Can I use g_anaeig -v Prt_MD_Eigenvec.trr -s Prt.tpr -f crystal.pdb -proj 12.xvg -n Prt_CA.ndx -first 1 -last 2 -2d 2dproj.xvg to obtain the crystal structure position? Or do I need to calculate covariance matrix for the crystal str.(I need a set of them in that case) and then use g_anaeig? Thanks a lot in advance. Regards, Anirban -- 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 -- Tsjerk A. Wassenaar, Ph.D. -- 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] Projection of crystal structure on PCA plot
Dear Tsjerk, Thank you very much for the explanation. So, in other words, as I have carried out PCA on the basis of CA atoms from the MD trajectory, so if I wish to project the crystal structure onto the EV, then I need to consider only the CA atoms of the crystal structure (which in that case won't be the exact crystal structure) as well. Right? Thanks a lot again. Regards, Anirban On Thu, Jun 6, 2013 at 3:56 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Anirban, The eigenvectors obtained from the simulation are a way of rewriting the coordinates of your structures, not in terms of atoms-XYZ, but as combinations of these. Because they are combinations of atom-positions, they are defined for the selection of atoms used for the calculation. If your crystal structure has the same atoms, which is true if you did not use hydrogen atoms, or modeled parts for the covariance analysis, then you can project that structure onto the eigenvectors determined, in exactly the way you describe in your question. Hope it helps, Tsjerk On Thu, Jun 6, 2013 at 12:06 PM, Anirban reach.anirban.gh...@gmail.com wrote: Hi ALL, I have carried out a simulation of a protein and have carried out PCA on the entire trajectory. I have obtained a 2D projection plot of EV1 on EV2. Now I want to locate the conformation of the crystal structure (with which I started the MD) on this map. How to do this? Can I use g_anaeig -v Prt_MD_Eigenvec.trr -s Prt.tpr -f crystal.pdb -proj 12.xvg -n Prt_CA.ndx -first 1 -last 2 -2d 2dproj.xvg to obtain the crystal structure position? Or do I need to calculate covariance matrix for the crystal str.(I need a set of them in that case) and then use g_anaeig? Thanks a lot in advance. Regards, Anirban -- 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 -- Tsjerk A. Wassenaar, Ph.D. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Projection of crystal structure on PCA plot
Hi Anirban, Indeed. :) Tsjerk On Thu, Jun 6, 2013 at 1:11 PM, Anirban reach.anirban.gh...@gmail.comwrote: Dear Tsjerk, Thank you very much for the explanation. So, in other words, as I have carried out PCA on the basis of CA atoms from the MD trajectory, so if I wish to project the crystal structure onto the EV, then I need to consider only the CA atoms of the crystal structure (which in that case won't be the exact crystal structure) as well. Right? Thanks a lot again. Regards, Anirban On Thu, Jun 6, 2013 at 3:56 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Anirban, The eigenvectors obtained from the simulation are a way of rewriting the coordinates of your structures, not in terms of atoms-XYZ, but as combinations of these. Because they are combinations of atom-positions, they are defined for the selection of atoms used for the calculation. If your crystal structure has the same atoms, which is true if you did not use hydrogen atoms, or modeled parts for the covariance analysis, then you can project that structure onto the eigenvectors determined, in exactly the way you describe in your question. Hope it helps, Tsjerk On Thu, Jun 6, 2013 at 12:06 PM, Anirban reach.anirban.gh...@gmail.com wrote: Hi ALL, I have carried out a simulation of a protein and have carried out PCA on the entire trajectory. I have obtained a 2D projection plot of EV1 on EV2. Now I want to locate the conformation of the crystal structure (with which I started the MD) on this map. How to do this? Can I use g_anaeig -v Prt_MD_Eigenvec.trr -s Prt.tpr -f crystal.pdb -proj 12.xvg -n Prt_CA.ndx -first 1 -last 2 -2d 2dproj.xvg to obtain the crystal structure position? Or do I need to calculate covariance matrix for the crystal str.(I need a set of them in that case) and then use g_anaeig? Thanks a lot in advance. Regards, Anirban -- 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 -- Tsjerk A. Wassenaar, Ph.D. -- 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 -- Tsjerk A. Wassenaar, Ph.D. -- 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] Projection of crystal structure on PCA plot
Thanks a lot Tsjerk :) -Anirban On Thu, Jun 6, 2013 at 4:42 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Anirban, Indeed. :) Tsjerk On Thu, Jun 6, 2013 at 1:11 PM, Anirban reach.anirban.gh...@gmail.com wrote: Dear Tsjerk, Thank you very much for the explanation. So, in other words, as I have carried out PCA on the basis of CA atoms from the MD trajectory, so if I wish to project the crystal structure onto the EV, then I need to consider only the CA atoms of the crystal structure (which in that case won't be the exact crystal structure) as well. Right? Thanks a lot again. Regards, Anirban On Thu, Jun 6, 2013 at 3:56 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Anirban, The eigenvectors obtained from the simulation are a way of rewriting the coordinates of your structures, not in terms of atoms-XYZ, but as combinations of these. Because they are combinations of atom-positions, they are defined for the selection of atoms used for the calculation. If your crystal structure has the same atoms, which is true if you did not use hydrogen atoms, or modeled parts for the covariance analysis, then you can project that structure onto the eigenvectors determined, in exactly the way you describe in your question. Hope it helps, Tsjerk On Thu, Jun 6, 2013 at 12:06 PM, Anirban reach.anirban.gh...@gmail.com wrote: Hi ALL, I have carried out a simulation of a protein and have carried out PCA on the entire trajectory. I have obtained a 2D projection plot of EV1 on EV2. Now I want to locate the conformation of the crystal structure (with which I started the MD) on this map. How to do this? Can I use g_anaeig -v Prt_MD_Eigenvec.trr -s Prt.tpr -f crystal.pdb -proj 12.xvg -n Prt_CA.ndx -first 1 -last 2 -2d 2dproj.xvg to obtain the crystal structure position? Or do I need to calculate covariance matrix for the crystal str.(I need a set of them in that case) and then use g_anaeig? Thanks a lot in advance. Regards, Anirban -- 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 -- Tsjerk A. Wassenaar, Ph.D. -- 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 -- Tsjerk A. Wassenaar, Ph.D. -- 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] Is non-linear data output/storage possible?
Hi everybody! This is a sort-of general question that I am not sure where to find the answer for. I am running a simulation on the order of tens of microseconds. However I also want to do some analysis on the order of very small time steps but I do not want to save the data of very small time steps throughout the length of the simulation as it will be taxing for the memory. I was wondering if there was a way to be able to store small time steps for a small time during the simulation and continue to increase the amount of time that energy/forces/coordinates are written and stored? I understand the mdp files control the output, but I do not know how to have a non-linear output of data using nstxout etc. Please let me know if you have any ideas/have succeeded in getting Gromacs to do this! -- View this message in context: http://gromacs.5086.x6.nabble.com/Is-non-linear-data-output-storage-possible-tp5008858.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] cg Fatal error--DD cell
1)I use steepest to minimize energy, .mdp as follows, title = bovin cpp = /usr/bin/cpp ; the c pre-processor define = -DFLEXIBLE constraints = all-bonds integrator = steep dt = 0.002; ps ! nsteps = 2000 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 vdwtype = cut-off rvdw= 1.4 fourierspacing= 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; ;Energy minimizing stuff ; emtol = 1000.0 emstep =0.01 ; GENERATE VELOCITIES FOR STARTUP RUN gen-vel = no gen-temp = 293 gen-seed = 173529 2) then I use cg do energy minimization, .mdp as follows, title = bovin cpp = /usr/bin/cpp define = -DFLEXIBLE constraints = all-bonds integrator = cg dt = 0.002; ps ! nsteps = 1000 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 vdwtype = cut-off rvdw= 1.4 fourierspacing= 0.12 fourier_nx= 0 fourier_ny= 0 fourier_nz= 0 pme_order= 4 ewald_rtol= 1e-5 optimize_fft= yes emtol = 100.0 emstep = 0.01 ; GENERATE VELOCITIES FOR STARTUP RUN gen-vel = no gen-temp = 293 gen-seed = 173529 both constraint all bond, 1) steepest is no problem; but 2) some error take place at cg I use grompp_d -f em_cg_constrain.mdp -c em.pdb -p topol.top -o bovin_em_cg.tpr mdrun_d -v -s bovin_em_cg.tpr -deffnm em_cg Starting 16 threads, ... Fatal error: DD cell 1 4 0 could only obtain 14 of the 16 atoms that are connected via constraints from the neighboring cells. This probably means your constraint lengths are too long compared to the domain decomposition cell size. Decrease the number of domain decomposition grid cells or lincs-order. at em_cg.log , maximum distance required for P-LINCS: 0.876 nm So, I revised the mdrun, mdrun_d -v -s bovin_em_cg.tpr -deffnm em_cg -nt 2 -rcon 0.876 nm -dds 0.876 another error take place, Fatal error: Too many LINCS warnings (1011) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem So, is anyway to resolve it ? I have try, but can not find the way. Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/cg-Fatal-error-DD-cell-tp5008859.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] No default Ryckaert-Bell. types
Hello, I am getting No default Ryckaert-Bell. types error for grompp. I have define all this parameter in .itp file Here is .itp file ; For parameters see J. Phys. Chem. A. 2002, 106, 1074-1080 ; Derived from parsing of runfiles/alat.top.orig ;[ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ ;1 3 yes 0.5 0.5 ; comb-rule 3 is square-root sigma, the OPLSAA version [ atomtypes ] ; full atom descriptions are available in ffoplsaa.atp ; name bond_typemasscharge ptype sigma epsilon opls_124 S 1632.06000 0.312 A3.56000e-01 1.65268e+00 opls_125 O 8 15.99940-0.556 A 2.93000e-01 1.17152e+00 opls_126 CT 6 15.03500-0.148 A 3.81000e-01 6.69440e-01 opls_140 HC 1 1.00800 0.090 A2.5e-01 1.25520e-01 [ bondtypes ] ; ij func b0 kb S O 10.1530 225936.0 S CT 10.1800 100416.0 CTHC 10.1110 134724.8 [ angletypes ] ; ijk func th0 cth CT S CT 195.0 142.256 CT S O 1 106.75 330.536 S CT HC 1 111.3 192.8824 HC CT HC 1 108.4 148.532 [ dihedraltypes ] ; ijkl func coefficients ; OPLS Fourier dihedraltypes translated to Gromacs Ryckaert-Bellemans form ; according to the formula in the Gromacs manual. CT S CT HC 3 1.35352 4.06057 0.0 -5.41410 0.0 0.0 ; sulfide all-atom O S CT HC 3 0.0 0.0 0.0 0.0 0.0 0.0 ; small ring Why I am getting this error. I am using Gromacs VERSION 4.0.7. Thanks Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Eigenvector and eigenvalues
Hi, I wanted to know about the eigenvectors and eigenvalues. I recently performed the principal component analysis (only the backbone into consideration) on a trajectory of 2000 residues. I obtained 15641 eigenvectors and 17928 eigenvalues. There is a difference in the number, which I am not quite sure off (perhaps that has to do with eigenvalue for each eigenvector, and the eigenvector has 3 co-ordinates x,y,z. I know I may be wrong completely but since there are 15641 eigenvectors, then shouldn't there by only 15641 eigenvalues for those eigenvectors) My second problem lies that I am trying to extract information or say RMSF values for the first 10 eigenvectors (10 slowest modes) and the last 10 eigenvectors (fastest modes) and there I face segmentation fault. I can get information on the first 10 but when I try last 10 with the command as follows: g_anaeig -v eigenvec.trr -eig eigenval.xvg -rmsf eig_rmsf.xvg -first 15631 [where -first should have the starting eigenvector ] (I choose, 15631 since I want the plot for last 10 but I get segmentation fault, which is also to do with the fact that the eigenval.xvg has 17928 values. This number doesn't match and so, maybe the plot is from 15631-17928). This has further confused me about the slowest and fastest modes (and somehow I do need information on the first 10 slowest modes and 10 fastest modes). In a broad way, the slowest modes would be the ones with high eigenvalues say, first 10 eigenvectors in eigenval.xvg would give the slowest 10 modes and the last 10 in eigenval.xvg should give the fastest 10 modes. Here, again I feel quite confused because eigenval.xvg has 17928 entries and in the legend, it says that x axis is the eigenvector index and y axis is eigenvalue index so it leaves me quite perplexed about the problem. I am sorry for this extremely long and confusing post, but any help in this regard would be really beneficial. Kind regards, Ankita -- Ankita Naithani -- 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] Eigenvector and eigenvalues
Hi Ankita, Please provide the commands you've run and the screen output from g_covar. Cheers, Tsjerk On Thu, Jun 6, 2013 at 3:44 PM, Ankita naithani ankitanaith...@gmail.comwrote: Hi, I wanted to know about the eigenvectors and eigenvalues. I recently performed the principal component analysis (only the backbone into consideration) on a trajectory of 2000 residues. I obtained 15641 eigenvectors and 17928 eigenvalues. There is a difference in the number, which I am not quite sure off (perhaps that has to do with eigenvalue for each eigenvector, and the eigenvector has 3 co-ordinates x,y,z. I know I may be wrong completely but since there are 15641 eigenvectors, then shouldn't there by only 15641 eigenvalues for those eigenvectors) My second problem lies that I am trying to extract information or say RMSF values for the first 10 eigenvectors (10 slowest modes) and the last 10 eigenvectors (fastest modes) and there I face segmentation fault. I can get information on the first 10 but when I try last 10 with the command as follows: g_anaeig -v eigenvec.trr -eig eigenval.xvg -rmsf eig_rmsf.xvg -first 15631 [where -first should have the starting eigenvector ] (I choose, 15631 since I want the plot for last 10 but I get segmentation fault, which is also to do with the fact that the eigenval.xvg has 17928 values. This number doesn't match and so, maybe the plot is from 15631-17928). This has further confused me about the slowest and fastest modes (and somehow I do need information on the first 10 slowest modes and 10 fastest modes). In a broad way, the slowest modes would be the ones with high eigenvalues say, first 10 eigenvectors in eigenval.xvg would give the slowest 10 modes and the last 10 in eigenval.xvg should give the fastest 10 modes. Here, again I feel quite confused because eigenval.xvg has 17928 entries and in the legend, it says that x axis is the eigenvector index and y axis is eigenvalue index so it leaves me quite perplexed about the problem. I am sorry for this extremely long and confusing post, but any help in this regard would be really beneficial. Kind regards, Ankita -- Ankita Naithani -- 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 -- Tsjerk A. Wassenaar, Ph.D. -- 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] Getting .edr file data as a generic data file
Hi again! At the moment, the only way I know how to access .edr files is through the use of g_energy. However g_energy only outputs .xvg files which is fine for routine analysis. However if I want to get into further processing, it would be helpful if I could get the information stored in the .edr files in a more pliable format. Please let me know if you know how to do this! I am a completely new user to Gromacs and appreciate all the help possible. -Neha -- View this message in context: http://gromacs.5086.x6.nabble.com/Getting-edr-file-data-as-a-generic-data-file-tp5008863.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] Segmentation fault (core dumped)
On 6/6/13 4:45 AM, Ishwor Poudyal wrote: Dear all I want to study the diffusion coeffcient of CO in water. I have done the energy minimization step and got the problem segmentation fault during Equilibration. I am confused whether my input file has got some error or the error is in the processing machine.I have made the following .mdp file ; ;PREPROCESSING parameters cpp = /lib/cpp define = -DFLEX_SPCE Here's the first suspect. The water models in Gromacs were intended to be rigid. Flexibility should only be used during EM, and only if necessary to improve the outcome. Running MD with flexible water is not advised. integrator = md dt =.002 nsteps = 2500 nstcomm = 1 ;OUPUT CONTROL parameters. nstxout = 250 nstvout = 1000 nstfout = 0 nstlog = 100 nstenergy = 100 energygrps = system ;NEIGHBOUR SEARCHING parameters. nstlist = 10 ns_type = grid rlist = 1.0 ;ELECTROSTATIC and VdW parameters. rcoulomb= 1.0 rvdw= 1.0 epsilon-r = 1 ;BERENDSEN TEMPERATURE COUPLING is on in two groups Tcoupl = berendsen tc-grps = system tau_t = 0.01 This is a very restrictive value of tau_t. Normally something like 0.1 or 0.5 is more appropriate. ref_t = 300 ;PRESSURE COUPLING is on Pcoupl = berendsen tau_p = 0.1 Again, very restrictive, especially for pressure. Try 1.0 or 2.0 instead. compressibility = 4.6e-5 ref_p = 1.0 ;SIMULATED ANNEALING parameters are not specified. ;GENERATE VELOCITIES is on at 300 K. gen_vel = yes; ; generate initially gen_temp= 300 gen_seed= 173259 ;give different values for different trials. ;BONDS parameters pbc = xyz ; 3-D PBC constraints = all-bonds constraint-algorithm = shake unconstrained-start = no The box size is 2.1 nm. You're playing with fire here - if the box deviates just a little bit due to pressure oscillations, your 1.0 nm will begin to double-count interactions and violate the minimum image convention. In that case, your trajectory is junk. -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] Re: pullx file content with pull_geometry = position
On 6/6/13 5:17 AM, Bastien Loubet wrote: I update the post to say that we tried to make a rerun of the trajectory on our local machine and the output of the pullx.xvg file (created with the option -px of mdrun) is: # This file was created Wed Jun 5 12:15:49 2013 # by the following command: # mdrun -s ../conf10.tpr -rerun ../conf10.xtc -px pullx_conf10.xvg -pf pullf_conf10.xvg -nt 6 -v # # mdrun is part of G R O M A C S: # # Gravel Rubs Often Many Awfully Cauterized Sores # @title Pull COM @xaxis label Time (ps) @yaxis label Position (nm) @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend 0 X @ s1 legend 0 Y @ s2 legend 0 Z @ s3 legend 1 dX @ s4 legend 1 dY @ s5 legend 1 dZ 0. 3.47835 5.10501 11.644 -0.378345 1.13499 1.73604 20. 3.47852 5.12016 11.6554 -0.446518 1.07184 1.69255 40. 3.49803 5.12013 11.6612 -0.350032 1.12387 1.75475 (...) ** The output of the pullx.xvg file is indeed the distance between the two pull groups, but this is very different numbers than the one obtained during the simulation on a cluster (see above post). So the question stand what are the numbers given in the pullx.xvg file created during the original simulation ? http://lists.gromacs.org/pipermail/gmx-users/2009-June/042887.html -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] No default Ryckaert-Bell. types
On 6/6/13 9:22 AM, Nilesh Dhumal wrote: Hello, I am getting No default Ryckaert-Bell. types error for grompp. I have define all this parameter in .itp file Here is .itp file ; For parameters see J. Phys. Chem. A. 2002, 106, 1074-1080 ; Derived from parsing of runfiles/alat.top.orig ;[ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ ;1 3 yes 0.5 0.5 ; comb-rule 3 is square-root sigma, the OPLSAA version [ atomtypes ] ; full atom descriptions are available in ffoplsaa.atp ; name bond_typemasscharge ptype sigma epsilon opls_124 S 1632.06000 0.312 A3.56000e-01 1.65268e+00 opls_125 O 8 15.99940-0.556 A 2.93000e-01 1.17152e+00 opls_126 CT 6 15.03500-0.148 A 3.81000e-01 6.69440e-01 opls_140 HC 1 1.00800 0.090 A2.5e-01 1.25520e-01 [ bondtypes ] ; ij func b0 kb S O 10.1530 225936.0 S CT 10.1800 100416.0 CTHC 10.1110 134724.8 [ angletypes ] ; ijk func th0 cth CT S CT 195.0 142.256 CT S O 1 106.75 330.536 S CT HC 1 111.3 192.8824 HC CT HC 1 108.4 148.532 [ dihedraltypes ] ; ijkl func coefficients ; OPLS Fourier dihedraltypes translated to Gromacs Ryckaert-Bellemans form ; according to the formula in the Gromacs manual. CT S CT HC 3 1.35352 4.06057 0.0 -5.41410 0.0 0.0 ; sulfide all-atom O S CT HC 3 0.0 0.0 0.0 0.0 0.0 0.0 ; small ring Why I am getting this error. Apparently grompp is failing to find some needed parameter. You should get a line number in the topology where this is occurring, which will allow you to map back the atoms involved. -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] No default Ryckaert-Bell. types
I checked the line number in .top file. Its not reading any dihedral parameter defined in .itp file. NIlesh On 6/6/13 9:22 AM, Nilesh Dhumal wrote: Hello, I am getting No default Ryckaert-Bell. types error for grompp. I have define all this parameter in .itp file Here is .itp file ; For parameters see J. Phys. Chem. A. 2002, 106, 1074-1080 ; Derived from parsing of runfiles/alat.top.orig ;[ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ ;1 3 yes 0.5 0.5 ; comb-rule 3 is square-root sigma, the OPLSAA version [ atomtypes ] ; full atom descriptions are available in ffoplsaa.atp ; name bond_typemasscharge ptype sigma epsilon opls_124 S 1632.06000 0.312 A3.56000e-01 1.65268e+00 opls_125 O 8 15.99940-0.556 A 2.93000e-01 1.17152e+00 opls_126 CT 6 15.03500-0.148 A 3.81000e-01 6.69440e-01 opls_140 HC 1 1.00800 0.090 A2.5e-01 1.25520e-01 [ bondtypes ] ; ij func b0 kb S O 10.1530 225936.0 S CT 10.1800 100416.0 CTHC 10.1110 134724.8 [ angletypes ] ; ijk func th0 cth CT S CT 195.0 142.256 CT S O 1 106.75 330.536 S CT HC 1 111.3 192.8824 HC CT HC 1 108.4 148.532 [ dihedraltypes ] ; ijkl func coefficients ; OPLS Fourier dihedraltypes translated to Gromacs Ryckaert-Bellemans form ; according to the formula in the Gromacs manual. CT S CT HC 3 1.35352 4.06057 0.0 -5.41410 0.0 0.0 ; sulfide all-atom O S CT HC 3 0.0 0.0 0.0 0.0 0.0 0.0 ; small ring Why I am getting this error. Apparently grompp is failing to find some needed parameter. You should get a line number in the topology where this is occurring, which will allow you to map back the atoms involved. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] No default Ryckaert-Bell. types
On 6/6/13 11:52 AM, Nilesh Dhumal wrote: I checked the line number in .top file. Its not reading any dihedral parameter defined in .itp file. Well, if it's not reading parameters, then that explains the error that tells you there are no parameters defined. -Justin On 6/6/13 9:22 AM, Nilesh Dhumal wrote: Hello, I am getting No default Ryckaert-Bell. types error for grompp. I have define all this parameter in .itp file Here is .itp file ; For parameters see J. Phys. Chem. A. 2002, 106, 1074-1080 ; Derived from parsing of runfiles/alat.top.orig ;[ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ ;1 3 yes 0.5 0.5 ; comb-rule 3 is square-root sigma, the OPLSAA version [ atomtypes ] ; full atom descriptions are available in ffoplsaa.atp ; name bond_typemasscharge ptype sigma epsilon opls_124 S 1632.06000 0.312 A3.56000e-01 1.65268e+00 opls_125 O 8 15.99940-0.556 A 2.93000e-01 1.17152e+00 opls_126 CT 6 15.03500-0.148 A 3.81000e-01 6.69440e-01 opls_140 HC 1 1.00800 0.090 A2.5e-01 1.25520e-01 [ bondtypes ] ; ij func b0 kb S O 10.1530 225936.0 S CT 10.1800 100416.0 CTHC 10.1110 134724.8 [ angletypes ] ; ijk func th0 cth CT S CT 195.0 142.256 CT S O 1 106.75 330.536 S CT HC 1 111.3 192.8824 HC CT HC 1 108.4 148.532 [ dihedraltypes ] ; ijkl func coefficients ; OPLS Fourier dihedraltypes translated to Gromacs Ryckaert-Bellemans form ; according to the formula in the Gromacs manual. CT S CT HC 3 1.35352 4.06057 0.0 -5.41410 0.0 0.0 ; sulfide all-atom O S CT HC 3 0.0 0.0 0.0 0.0 0.0 0.0 ; small ring Why I am getting this error. Apparently grompp is failing to find some needed parameter. You should get a line number in the topology where this is occurring, which will allow you to map back the atoms involved. -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 -- 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] mdrun segmentation fault for new build of gromacs 4.6.1
Gromacs users: I have just built and installed gromacs-4.6.1 on my Xeon 5500 compute cluster running Centos 5. The installation was done with gcc 4.7.0 I have run a simple test (the old tutor/gmxdemo) which fails at the first mdrun step with a segmentation fault. The command line for this step is: mdrun -nt 1 -s cpeptide_em -o cpeptide_em -c cpeptide_b4pr -v -debug 1 where I have included the debug flag and have restricted the run to one core. The files associated with this run are located at: https://www.dropbox.com/sh/h6867f7ivl5pcl9/j9gt9CsVdP I have done a test build of gromacs-4.5.4 (version I have been running the last year) with the same build environment as the 4.6.1 build, including using cmake. The rebuild of gromacs-4.5.4 runs the demo completely. Given the limited information for the run (segmentation fault seems to occur just after reading in the parameters), I'm not sure how to further pursue the source of this error. I have also tried building gromacs-4.6.2 but have the same error for mdrun. Thanks for any insight that you may be able to provide. Dr. Amil Anderson Associate Professor of Chemistry Wittenberg University -- 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: cg Fatal error--DD cell
the information on .log as follows: Initializing Domain Decomposition on 2 nodes Dynamic load balancing: no Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 0.598 nm, LJ-14, atoms 942 950 multi-body bonded interactions: 0.598 nm, Proper Dih., atoms 942 950 Minimum cell size due to bonded interactions: 0.657 nm User supplied maximum distance required for P-LINCS: 0.876 nm Using 0 separate PME nodes Optimizing the DD grid for 2 cells with a minimum initial size of 0.876 nm The maximum allowed number of cells is: X 7 Y 7 Z 7 Domain decomposition grid 2 x 1 x 1, separate PME nodes 0 PME domain decomposition: 2 x 1 x 1 Domain decomposition nodeid 0, coordinates 0 0 0 Table routines are used for coulomb: TRUE Table routines are used for vdw: FALSE Will do PME sum in reciprocal space. Anybody could tell me how to fix this problem! Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/cg-Fatal-error-DD-cell-tp5008859p5008875.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] xx of the xxxx bonded interactions couldn't be calculated
Dear GMX-users Recently i got this error and note from my MD2 simulation. I'm solvating 1-octanol to 1-octanol and calculating free energy differences. This is the last step of my calculation and previous steps are looking fine. Basically i followed Justin's free energy tutorial. Here is Note: A list of missing interactions: LJC Pairs NB of210 missing 1 exclusions of 25308 missing 1 Molecule type '1-octanol' the first 10 missing interactions, except for exclusions: LJC Pairs NB atoms3 25 global 325 Fatal error: 2 of the 57736 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1 nm) or the two-body cut-off distance (1 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck Please help me and suggest any idea to solve this problem? -- View this message in context: http://gromacs.5086.x6.nabble.com/xx-of-the--bonded-interactions-couldn-t-be-calculated-tp5008876.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] xx of the xxxx bonded interactions couldn't be calculated
On 6/6/13 10:00 PM, Badamkhatan wrote: Dear GMX-users Recently i got this error and note from my MD2 simulation. I'm solvating 1-octanol to 1-octanol and calculating free energy differences. This is the last step of my calculation and previous steps are looking fine. Basically i followed Justin's free energy tutorial. Here is Note: A list of missing interactions: LJC Pairs NB of210 missing 1 exclusions of 25308 missing 1 Molecule type '1-octanol' the first 10 missing interactions, except for exclusions: LJC Pairs NB atoms3 25 global 325 Fatal error: 2 of the 57736 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1 nm) or the two-body cut-off distance (1 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck Please help me and suggest any idea to solve this problem? Sounds like you're 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
RE: [gmx-users] Is non-linear data output/storage possible?
Easiest, naïve way that I can see is to do the simulation in blocks, and change the output settings within the mdp file used as required for each block. Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Neha Sent: Thursday, 6 June 2013 11:00 PM To: gmx-users@gromacs.org Subject: [gmx-users] Is non-linear data output/storage possible? Hi everybody! This is a sort-of general question that I am not sure where to find the answer for. I am running a simulation on the order of tens of microseconds. However I also want to do some analysis on the order of very small time steps but I do not want to save the data of very small time steps throughout the length of the simulation as it will be taxing for the memory. I was wondering if there was a way to be able to store small time steps for a small time during the simulation and continue to increase the amount of time that energy/forces/coordinates are written and stored? I understand the mdp files control the output, but I do not know how to have a non-linear output of data using nstxout etc. Please let me know if you have any ideas/have succeeded in getting Gromacs to do this! -- View this message in context: http://gromacs.5086.x6.nabble.com/Is-non- linear-data-output-storage-possible-tp5008858.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] mdrun segmentation fault for new build of gromacs 4.6.1
Hi, I recommend to run the regressiontests. The simplest way is to build GROMACS with cmake -DREGRESSIONTEST_DOWNLOAD, and run make check. See http://www.gromacs.org/Documentation/Installation_Instructions#.c2.a7_4.12._Testing_GROMACS_for_correctness for more details. Roland On Thu, Jun 6, 2013 at 4:56 PM, Amil G. Anderson aander...@wittenberg.edu wrote: Gromacs users: I have just built and installed gromacs-4.6.1 on my Xeon 5500 compute cluster running Centos 5. The installation was done with gcc 4.7.0 I have run a simple test (the old tutor/gmxdemo) which fails at the first mdrun step with a segmentation fault. The command line for this step is: mdrun -nt 1 -s cpeptide_em -o cpeptide_em -c cpeptide_b4pr -v -debug 1 where I have included the debug flag and have restricted the run to one core. The files associated with this run are located at: https://www.dropbox.com/sh/h6867f7ivl5pcl9/j9gt9CsVdP I have done a test build of gromacs-4.5.4 (version I have been running the last year) with the same build environment as the 4.6.1 build, including using cmake. The rebuild of gromacs-4.5.4 runs the demo completely. Given the limited information for the run (segmentation fault seems to occur just after reading in the parameters), I'm not sure how to further pursue the source of this error. I have also tried building gromacs-4.6.2 but have the same error for mdrun. Thanks for any insight that you may be able to provide. Dr. Amil Anderson Associate Professor of Chemistry Wittenberg University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Unable to download Gromacs source tar file
Hi, I would like to use Gromacs for MD simulation of biomolecules. But I am not able to download any of the source files from the link http://www.gromacs.org/Downloads Can anyone please help. Thanks and regards, Maithry -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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] Regarding mdrun
Dear gmx-users, I am experiencing some strange things while performing mdrun. I am running a CG simulation and it is terminating with LINCS warnings after approx. 500ns of simulation. If I restart it with the check point file, then its running with out any errors. Is my simulation is reliable?? I am using Gromacs-4.5.5. Thank you -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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
