Re: [gmx-users] missing of methyl at N-terminal
I have had trouble capping N- and C- terminal residues using the 3.3.X series of GROMACS. I even think I started a thread about it. Before you digg that thread up you should: i) work out what you want to do ii) understand what result you should get iii) do it and check it !!! If that fails I suggest you search the list for archives for threads discussing capping problems. For the record I got around the problem using pdb2gmx from the 3.2 or 3.1 series of GROMACS. Cheers Mitch Mark Abraham wrote: Bhawana Gupta wrote: hello, thankyou for ur advice on the mail named *missing of methyl at N-terminal. Terminology is important to get right. You were capping the *C-terminal* end with an *N-methyl*. * i m using forcefield ffgmx. That's a poor idea for anything other than a learning exercise. That force field has been deprecated for years. u had advice me to put the correct name for terminal N-CH3 group i.e. i had replaced NHM with NAC as given there. That error has been solved but again i m getting the error as: - Program pdb2gmx, VERSION 4.0 Source code file: pdb2top.c, line: 574 Fatal error: atom N not found in residue 1ACE while combining tdb and rtp - This is my pdb file in text editor So what were your pdb2gmx command line and responses to prompts? You need to think carefully about why pdb2gmx might be looking for an N atom in your ACE residue that doesn't have one. Mark ___ 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 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
Re: [gmx-users] Gromacs-4.0.2 is out
Hi, Thanks for the release. I notice that the modifications I sent for trjconv didn't make it. For those who are interested, replacing the distribution gmx_trjconv.c with the one attached will add the molecular shaped box to the unit cell options. This allows distributing the solvent around a solute, bring the ligand inside the protein, etc. Moreover, this version asks which group you want to apply the -pbc nojump/inbox operation on, so you can keep your dimer together and keep the solvent from wandering away. Cheers, Tsjerk On Mon, Nov 10, 2008 at 9:23 AM, Erik Lindahl [EMAIL PROTECTED] wrote: Hi, I think we've fixed all minor issues with Gromacs-4.0 now; please download the new release from ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.0.2.tar.gz Now, a friend of order might ask what happened to 4.0.1 that appeared on the ftp site for a couple of hours on friday? Unfortunately we accidentally disabled all water optimization in that brown-paper-bag-over-head release, which will result in a serious performance drop. Thus, PLEASE UPGRADE TO 4.0.2 ASAP IF YOU INSTALLED 4.0.1! Sorry for the confusion - now that we have a somewhat stable release we'll concentrate on creating binary packages! Cheers, Erik ___ 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 thewww interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 gmx_trjconv.c.gz Description: GNU Zip compressed data ___ 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] Water model = amber port to gromacs ? = OR
HI The thing is the definition of atom type, OW and H in gromos 96 are different from tip3p.itp, OWT3, HW. same thing as other tip*p.itp. How to fix this? Thank you Lin ___ 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
RE: [gmx-users] .mdp file
You have to modify the input .mdp and run grompp again. The mdout.mdp is for information only. Andreas -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Andrea Muntean Sent: 10 November 2008 12:42 To: Gromacs Users' List Subject: [gmx-users] .mdp file Hello there, I have a practical question regarding the mdp file, regardless the system to simulate. Before I would run a md simulation, usually we have to run grompp in order to preprocess the system. So I obtain, among other files, the mdout.mdp, based on the input mdp file. My question: If I want to run another simulation, with the same input, only with small changes in the mdp file (like number of steps or so), do I have to each time modify the input .mdp and run grompp, or is it enough if I modify mdout.mdp? Best regards, Andrea ___ 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 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
Re: [gmx-users] adding NH2 cap to C terminal
sarbani chattopadhyay wrote: Thank you for reply. Amber force fields have parameters for C-terminal-C(O)-NH2 . But I don't know which of the force fields in Gromacs 3.3.1 have parametrs for the C-terminal amide cap. Check out the .rtp file. That's how GROMACS knows what it has parameters for. Is it possible to introduce these parameters manually. What I need to know is that which other files do I need to modify ? Potentially, none. Till now I have only modified the terminal database ,( though I may have made some mistake ), but the added N 's coordinates are given by pdb2gmx as nan nan nan Depending on your need, making a custom residue type in the .rtp database, or a custom terminus in the .tdb database might work. Either way, Chapter 5 is your friend. Mark ___ 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
Re: [gmx-users] .mdp file
I thought so. Thank you very much! Cheers Andrea 2008/11/10 Justin A. Lemkul [EMAIL PROTECTED]: Andrea Muntean wrote: Hello there, I have a practical question regarding the mdp file, regardless the system to simulate. Before I would run a md simulation, usually we have to run grompp in order to preprocess the system. So I obtain, among other files, the mdout.mdp, based on the input mdp file. My question: If I want to run another simulation, with the same input, only with small changes in the mdp file (like number of steps or so), do I have to each time modify the input .mdp and run grompp, or is it enough if I modify mdout.mdp? No. The mdout.mdp file is output, a record of all the simulation parameters, including the ones you accepted as defaults by not explicitly entering into your grompp.mdp file (the input). If you want to run different simulations, you need to modify your input, or else these new parameters will never reach the .tpr file and you will be running the same thing over and over again. -Justin Best regards, Andrea ___ 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 -- Justin A. Lemkul Graduate Research Assistant 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://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 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
Re: [gmx-users] Re: Spatial distibution
Gadzikano Munyuki wrote: I have checked the source code and it looks like g_spatial has been replaced by g_cluster.I got the code below under g_spatial.c OK, good trouble-shooting. I filed a bugzilla for you. Note that your output from g_spatial -h would have matched that from g_cluster -h which would have helped diagnose the problem. Mark ___ 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
Re: [gmx-users] files to modify to add NH2 cap at C terminal end
sarbani chattopadhyay wrote: Hi everyone, I had asked this question before but I will try to explain myself more clearly. I wan t to add -NH2 cap at the Cterminal end of my protein. I had included charmm force field into my gromacs 3.3.1. I had added the following into my ffcharmm-c.tdb file [NH2] [replace] OOB15.994 -0.550 CACT112.0110 0.070 CCD12.0110 0.720 [add] 14NH2 C CA C NH2 14.0027 -0.7800 23HTN CA C HT 1.0080 0.3100 However, the coordinates of the added N is given by pdb2gmx as nan nan nan. nan = Not a Number, i.e. pdb2gmx was unable to compute the position of your N atom. The three control atoms i,j,k have to be different, since you need three unique pieces of information to isolate a point in 3D space. I'd be surprised if pdb2gmx didn't issue a warning about this, but perhaps the developers assumed that someone willing to edit the .tdb would get it right! Mark ___ 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
Re: [gmx-users] Gromacs-4.0.2 is out
On Mon, 2008-11-10 at 09:23 +0100, Erik Lindahl wrote: Hi, I think we've fixed all minor issues with Gromacs-4.0 now; please download the new release from Gromacs 4.0.2 Fedora packages have been built and will be released in the next Fedora / Fedora EPEL updates push (in a few days). If you have installed Gromacs 4.0 with yum the packages will update automatically. If you are interested in the SRPM you can get it e.g. from http://koji.fedoraproject.org/koji/ -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto [EMAIL PROTECTED], p. 191 50623 -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland [EMAIL PROTECTED] -- ___ 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
Re: [gmx-users] freeze group gives Segmentation fault
I just tried Gromacs 4.0.2. It still gives a Segmentation fault: Reading file topol.tpr, VERSION 4.0.2 (single precision) Loaded with Money Segmentation fault I did a test, putting the whole system into one freezegroup. Then the simulation starts running. But some of the atoms belonging to the freeze-group still move: The RMSD keeps growing and the Potential Energy = -132 kJ/mol. Reading in the trajectory with vmd shows the molecules moving. There is no pattern in the motion though. I checked the index.ndx twice - there is no mistake in there. Ilona There was a bug in the freeze group code that got fixed today. I don't know anything else about it. Please update your source code and try again. Mark [EMAIL PROTECTED] wrote: Using freezegroups I get a Segmentation fault. The simulation does not start, so the output is empty. Reading file topol.tpr, VERSION 4.0_rc4 (single precision) Segmentation fault ; ; File 'mdout.mdp' was generated ; By user: bq_ibaldus (2417) ; On host: cln-fg06 ; At date: Fri Nov 7 15:53:11 2008 ; ; VARIOUS PREPROCESSING OPTIONS ; Preprocessor information: use cpp syntax. ; e.g.: -I/home/joe/doe -I/home/mary/hoe include = ; e.g.: -DI_Want_Cookies -DMe_Too define = ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.002 nsteps = 500 ; For exact run continuation or redoing part of a run ; Part index is updated automatically on checkpointing (keeps files separate) simulation_part = 1 init_step= 0 ; mode for center of mass motion removal comm-mode= none ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= ; LANGEVIN DYNAMICS OPTIONS ; Friction coefficient (amu/ps) and random seed bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol= 0.01 emstep = 0.01 ; Max number of iterations in relax_shells niter= 100 ; Step size (ps^2) for minimization of flexible constraints fcstep = 0 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr= 10 ; TEST PARTICLE INSERTION OPTIONS rtpi = 0.05 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 1 nstvout = 1 nstfout = 1 ; Output frequency for energies to log file and energy file nstlog = 1 nstenergy= 500 ; Output frequency and precision for xtc file nstxtcout= 1000 xtc_precision= 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = ; Selection of energy groups energygrps = crystal ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 10 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz, no, xy pbc = xyz periodic_molecules = no ; nblist cut-off rlist= 1.5 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = cut-off rcoulomb_switch = 0 rcoulomb = 1.5 ; Relative dielectric constant for the medium and the reaction field epsilon_r= 1 epsilon_rf = 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw_switch = 0 rvdw = 1.5 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Seperate tables between energy group pairs energygrp_table = ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no ; IMPLICIT SOLVENT ALGORITHM implicit_solvent = No ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii =
Re: Re: [gmx-users] adding NH2 cap to C terminal
Thank you for reply. Amber force fields have parameters for C-terminal-C(O)-NH2 . But I don't know which of the force fields in Gromacs 3.3.1 have parametrs for the C-terminal amide cap. Is it possible to introduce these parameters manually. What I need to know is that which other files do I need to modify ? Till now I have only modified the terminal database ,( though I may have made some mistake ), but the added N 's coordinates are given by pdb2gmx as nan nan nan Thanks in advance Sarbani On Mon, 10 Nov 2008 Mark Abraham wrote : sarbani chattopadhyay wrote: Hi, I want to add -NH2 to the c terminal end of my peptide. If I modify the C-terminal databse- -c.tdb , will it be possible to add -NH2 to the CO end of the last residue at the C terminal end. For some forcefields, yes. You need the forcefield to have parameters for (C-terminal) -C (O)-NH2. Not all of them do. Probably the ones that have it parameterized already have the terminus topologies in the database. Mark ___ 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 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] [Fwd: Water model = amber port to gromacs ? = OR]
Original Message Subject: Water model = amber port to gromacs ? = OR Date: Mon, 10 Nov 2008 01:22:07 -0800 From: Chih-Ying Lin [EMAIL PROTECTED] To: [EMAIL PROTECTED] CC: gmx-users@gromacs.org HI The thing is the definition of atom type, OW and H in gromos 96 are different from tip3p.itp, OWT3, HW. same thing as other tip*p.itp. How to fix this? Thank you Lin - Please keep GROMACS correspondence on the mailing list. The atom type name doesn't matter for purposes of having a topology file that matches a coordinate file. Only the molecule ordering, atom ordering and atom names matter. Thus from a technical point of view, you could substitute any 3-centered water model that had the same atom names and ordering merely by substituting in and out the name of an .itp file, or using a #define. If you inspect tip3p.itp you will see that some of this chicanery is going on. It's conceivable the atom names differ for different water models. If you want to keep the same coordinates, then you'd best rename the atoms in the structure file. If you don't mind building different coordinates, then you can strip the waters away and re-invoke genbox. Mark ___ 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
Re: [gmx-users] gromacs parallel problem
mario ciappy wrote: Dear All, I configured gromacs 3.3.3 for parallel runs, using the precompiled packeges on ubuntu server 8.04, with LAM program 7.1.2 ( alreay present in server verison). I tried with d.villin benchmark but I detected an decrease of performance increasing the node's number. The obtained results for 1 node are: (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance: 6.686 1.437 8.471 2.833 The obtained results for 7 nodes are: (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance: 5.169 1.112 6.545 3.667 I have a cluster of 7 nodes (pentium 4 3.2 Ghz with RAM 2Gb) connected on 10/100 Mbps dual speed up hub. I don't know if it is a configuration problem (because with precompiled packages I couldn't use the configuration parameters described on web) or an hardware problem due to hub. One can get what one pays for with network hardware. Search in the archives for posts by Carsten Kutzner with lots of comments here. Mark ___ 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
Re: [gmx-users] Gromacs 4 Scaling Benchmarks...
Hi, most likely the Ethernet is the problem here. I compiled some numbers for the DPPC benchmark in the paper Speeding up parallel GROMACS on high-latency networks, http://www3.interscience.wiley.com/journal/114205207/abstract?CRETRY=1SRETRY=0 which are for version 3.3, but PME will behave similarly. If you did not already use separate PME nodes, this is worth a try, since on Ethernet the performance will drastically depend on the number of nodes involved in the FFT. I also have a tool which finds the optimal PME settings for a given number of nodes, by varying the number of PME nodes and the fourier grid settings. I can send it to you if you want. Carsten On Nov 9, 2008, at 10:30 PM, Yawar JQ wrote: I was wondering if anyone could comment on these benchmark results for the d.dppc benchmark? Nodes Cutoff (ns/day) PME (ns/day) 4 1.331 0.797 8 2.564 1.497 16 4.5 1.92 32 8.308 0.575 64 13.50.275 128 20.093 - 192 21.6- It seems to scale relatively well up to 32-64 nodes without PME. This seems slightly better than the benchmark results for Gromacs 3 on www.gromacs.org. Can someone comment on the magnitude of the performance hit and lack of scaling with PME is worrying me. For the PME runs, I set rlist,rvdw,rouloumb=1.2 and the rest set to the defaults. I can try it with some other settings, larger spacing for the grid, but I'm not sure how much more that would help. Is there a more standardized system I should use for testing PME scaling? This is with GNU compilers and parallelization with OpenMPI 1.2. I'm not sure what we're using for the FFTW The compute nodes are Dell m600 blades w/ 16GB of RAM and dual quad core Intel Xeon 3GHz processors. I believe it's all ethernet interconnects. Thanks, YQ ___ 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 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
RE: [gmx-users] Gromacs 4 Scaling Benchmarks...
The fftw used during compilation was FFTW 3.1.2 compiled using the GNU compilers. From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Yawar JQ Sent: Sunday, November 09, 2008 3:31 PM To: gmx-users@gromacs.org Subject: [gmx-users] Gromacs 4 Scaling Benchmarks... I was wondering if anyone could comment on these benchmark results for the d.dppc benchmark? Nodes Cutoff (ns/day) PME (ns/day) 4 1.331 0.797 8 2.564 1.497 16 4.5 1.92 32 8.308 0.575 64 13.5 0.275 128 20.093 - 192 21.6 - It seems to scale relatively well up to 32-64 nodes without PME. This seems slightly better than the benchmark results for Gromacs 3 on www.gromacs.org http://www.gromacs.org/ . Can someone comment on the magnitude of the performance hit and lack of scaling with PME is worrying me. For the PME runs, I set rlist,rvdw,rouloumb=1.2 and the rest set to the defaults. I can try it with some other settings, larger spacing for the grid, but I'm not sure how much more that would help. Is there a more standardized system I should use for testing PME scaling? This is with GNU compilers and parallelization with OpenMPI 1.2. I'm not sure what we're using for the FFTW The compute nodes are Dell m600 blades w/ 16GB of RAM and dual quad core Intel Xeon 3GHz processors. I believe it's all ethernet interconnects. Thanks, YQ ___ 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] temperature coupling strength
Deal all, Is there any practical approach to choose the right temperature coupling strength for a simulation? For example, if a system behaves differently with weak coupling and strong coupling, which result I should trust? Also, I thought giving a very weak nose-hoover thermostat coupling would be similar to the NVE simulation. However, when I run the simulation, the system behaves very weirdly by constantly accelerating and slowing down. will there be any explanation on this behavior? Thanks, Seunghyun ___ 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
Re: [gmx-users] Thickness distribution over area of bilayer-membrane
anirban polley wrote: Hi, I saw that average thickness can be measured by peak to peak distance of a electron density graph. This electron density can be calculated by g_density command. But g_density gives the average electron density of the membrane. So, I can get the average thickness of the membrane by subtracting peak to peak distance of the electron density graph. But I want to see how the thickness of the membrane is fluctuating over area. So, can you tell me how I can calculate the thickness of the membrane. Please see the message I just sent out, and have a look at the following link: http://www.bevanlab.biochem.vt.edu/GridMAT-MD/ -Justin Regards, Anirban ___ 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 -- Justin A. Lemkul Graduate Research Assistant 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://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] Announcing a new membrane analysis tool: GridMAT-MD
Hi All, I would like to announce the availability of a new program developed within our lab for membrane analysis, which we have named GridMAT-MD. The program measures bilayer thickness across the membrane, projected in the plane of the bilayer, as well as area per lipid. The program *does* account for the presence of membrane proteins. The algorithm and validation have been accepted by the Journal of Computational Chemistry, and the article is now in press, although it has not yet appeared in electronic format online. The program is written in Perl, and has been tested under all the major operating systems. Currently GridMAT-MD only supports the input of .gro files, but we expect to expand upon this shortly. Please feel free to download GridMAT-MD and test it; we are offering it for free under the terms and conditions of the GPL: http://www.bevanlab.biochem.vt.edu/GridMAT-MD We ask that you fill out a simple form when you download it, mostly to satisfy our own curiosity to know how many people are downloading it. If you have any questions about usage or if you run into any problems, please feel free to contact any of the developers, whose contact information can be found at the GridMAT-MD site. The tarball contains a PDF users' guide which should address many questions that may arise. Thanks, and we hope you enjoy our little program. -Justin -- Justin A. Lemkul Graduate Research Assistant 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://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] g_rms
Hi, i use g_rms to calculate rms, as reference structure (-s) i use myprotein.pdb file and trajectory (-f) is a trajectiry after MD MDprotein.pdb. The thing is that myprotein.pdb and MDprotein.pdb have the same atoms BUT their order within a residue is DIFFERENT. example: myprotein.pdb: ATOM 1 N ALA E 1 18.858 -22.883 26.306 1.00 0.00 ATOM 2 CA ALA E 1 19.106 -24.277 26.027 1.00 0.00 ATOM 3 C ALA E 1 20.206 -24.458 25.006 1.00 0.00 ATOM 4 O ALA E 1 20.156 -23.801 23.972 1.00 0.00 ATOM 5 CB ALA E 1 17.865 -24.819 25.301 1.00 0.00 MDprotein.pdb: ATOM 1 N ALA 1 18.861 24.179 26.290 1.00 0.00 ATOM 2 CA ALA 1 18.978 22.741 26.011 1.00 0.00 ATOM 3 CB ALA 1 17.670 22.190 25.440 1.00 0.00 ATOM 4 C ALA 1 20.069 22.592 24.949 1.00 0.00 ATOM 5 O ALA 1 20.120 23.450 24.070 1.00 0.00 whether g_rms work correct in this case? g_rms -s myprotein.pdb -f MDprotein.pdb ___ 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
Re: [gmx-users] files to modify to add NH2 cap at C terminal end
sarbani chattopadhyay wrote: Hi everyone, I had asked this question before but I will try to explain myself more clearly. I wan t to add -NH2 cap at the Cterminal end of my protein. I had included charmm force field into my gromacs 3.3.1. I had added the following into my ffcharmm-c.tdb file [NH2] [replace] OOB15.994 -0.550 CACT112.0110 0.070 CCD12.0110 0.720 [add] 14NH2 C CA C NH2 14.0027 -0.7800 I don't know what add type 4 is in the context of a C-terminal database, but in the .hdb it means to add two or three tetrahedral H atoms. 23HTN CA C HT 1.0080 0.3100 However, the coordinates of the added N is given by pdb2gmx as nan nan nan. Are they present in the input structure? If you're trying to add them through this mechanism, it probably won't work. If anyone can give any suggestion to fix this poblem, I will be highly obliged. The CHARMM .rtp that I have (from the User Contributions site) contains a parameterized NH2 residue. That means, if the amide is present in the .pdb file you have, then all you have to do is give pdb2gmx -ter and select 'None', instead of messing around with the .tdb files. -Justin Thanks in advance, Sarbani ___ 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 -- Justin A. Lemkul Graduate Research Assistant 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://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] questions in Running MDS over docked poses
Hi There, I am running MDS over the docked poses to check the stability of the docked poses using gromacs. I have few doubts about selecting parameters for the same, If anybody have tried such thing earlier, please suggest me for the same. Should I keep pressure coupling over the simulation ? For how long should I run the simulation for such purpose ? Waiting for suggestions. With Thanks, Vivek ___ 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] xdrf Fortran program and g_traj
Hi all, I was wondering if somebody has worked or used the xdrf Fortran program in order to read the coordinates from a .xtc file. There are 6 errors after compiling the program . The subroutines are not included there and I couldn't find them in the links - http://hpcv100.rc.rug.nl/xdrf.html , http://hpcv100.rc.rug.nl/xdrfman.html . I am simulating a solution in a confinement between two parallel walls and I want to check how many molecules are adsorbed to the walls. Therefore, I am trying to write a program to keep track of the molecules coordinates. Has anybody done something like this before? Did anybody use g_traj to read the coordinates? I can't understand what has been plotted, although I tried to plot z-component but the result of z-component is the same as that of x-component. I really appreciate if anybody can help me . Shaqa, MASc. Chemical Engineering Dalhousie University ___ 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
Re: [gmx-users] Parameters
On Mon, 10 Nov 2008 00:45:19 + andrea hanna [EMAIL PROTECTED] wrote: Dear users, I have performed a number of simulations using the ffG43a2 ff in 3.2.1 and the following parameters (only a few are given): ; RUN CONTROL PARAMETERS integrator = md tinit= 0 dt = 0.002 nsteps = 125000 comm-mode= Linear nstcomm = 1 nstlist = 10 ns-type = Grid pbc = xyz rlist= 1.0 domain-decomposition = no coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.0 epsilon-r= 1 vdw-type = Cut-off rvdw-switch = 0 rvdw = 1.0 I recently noticed from the manual that the nstlist should be 5 with gromos 96 ff. I have a couple of questions. 1. should this be 5 with a 0.001 timestep or with a 0.002 timestep 2. As I have done a lot of work using these parameters I was really looking for some suggestions/advice as to whether I can use any of my data - I;m really clinging onto hope here! And as to how 'badly' this choice/mistake will have affected my work. The nstlist is one issue but the most worrying is the use of a straight cutoff at 1.0 nm for the vdW. This should be 1.4 nm and makes a big difference. Note also that I am not sure this force field has not been tested for PME and developed for Reaction-Field. You should check the original paper. You can rerun some of your jobs with a parameter set closer to the original and check whether your observable vary significantly or not. That is probably the best you can do. XAvier. Thanks, Les - XAvier Periole - PhD - Molecular Dynamics Group - Computation and NMR University of Groningen The Netherlands - ___ 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
Re: [gmx-users] temperature coupling strength
On Mon, Nov 10, 2008 at 17:42, Seunghyun Chung [EMAIL PROTECTED] wrote: Deal all, Is there any practical approach to choose the right temperature coupling strength for a simulation? For example, if a system behaves differently with weak coupling and strong coupling, which result I should trust? In general, the coupling lifetime should not interfere with any fast degrees of motion you might have. For example, for pure water (where hydrogen bond lifetime is in the ps region, and OH vibration is in the fs lifetime), the thermostat coupling might be ~0.5 ps, but for a protein, perhaps a value in the area of 1 ps and above might be more suites. Plotting the temperature devations and/or averages might direct you to the better value. Also, I thought giving a very weak nose-hoover thermostat coupling would be similar to the NVE simulation. However, when I run the simulation, the system behaves very weirdly by constantly accelerating and slowing down. will there be any explanation on this behavior? I agree. But did you start applying the weak coupling before or after the system was already equilibrated? --Omer. ___ 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] gromacs parallel problem
Dear All, I configured gromacs 3.3.3 for parallel runs, using the precompiled packeges on ubuntu server 8.04, with LAM program 7.1.2 ( alreay present in server verison). I tried with d.villin benchmark but I detected an decrease of performance increasing the node's number. The obtained results for 1 node are: (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance: 6.686 1.437 8.471 2.833 The obtained results for 7 nodes are: (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance: 5.169 1.112 6.545 3.667 I have a cluster of 7 nodes (pentium 4 3.2 Ghz with RAM 2Gb) connected on 10/100 Mbps dual speed up hub. I don't know if it is a configuration problem (because with precompiled packages I couldn't use the configuration parameters described on web) or an hardware problem due to hub. Please can you help me? Is possible to improve performance changing some other parameters or configuration settings? Thank you in advance Best regards Mario Unisciti alla community di Io fotografo e video, il nuovo corso di fotografia di Gazzetta dello sport: http://www.flickr.com/groups/iofotografoevideo___ 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
Re: [gmx-users] adding NH2 cap to C terminal
sarbani chattopadhyay wrote: Thank you for reply. Amber force fields have parameters for C-terminal-C(O)-NH2 . But I don't know which of the force fields in Gromacs 3.3.1 have parametrs for the C-terminal amide cap. Is it possible to introduce these parameters manually. What I need to know is that which other files do I need to modify ? Till now I have only modified the terminal database ,( though I may have made some mistake ), but the added N 's coordinates are given by pdb2gmx as nan nan nan I think you are going about this the wrong way. The first question is - do you have the amide intact in the .pdb file? If not, pdb2gmx is not going to add it in for you magically. You can find out which force fields contain parameterized NH2 groups if you just search the .rtp files with a text editor. Offhand, I know that the Gromos force fields support C-terminal amides, but probably others do as well. -Justin Thanks in advance Sarbani On Mon, 10 Nov 2008 Mark Abraham wrote : sarbani chattopadhyay wrote: Hi, I want to add -NH2 to the c terminal end of my peptide. If I modify the C-terminal databse- -c.tdb , will it be possible to add -NH2 to the CO end of the last residue at the C terminal end. For some forcefields, yes. You need the forcefield to have parameters for (C-terminal) -C (O)-NH2. Not all of them do. Probably the ones that have it parameterized already have the terminus topologies in the database. Mark ___ 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 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 -- Justin A. Lemkul Graduate Research Assistant 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://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
Re: [gmx-users] bad box in protein.gro
Hi Alessandro, editconf encounters a bad box in the input file and I think it first replaces that with a standard box internally. Check the box at the end of box.gro to see if the result is what it should be (nine numbers, according to the specification of the rhombic dodecahedon in Chapter 3 of the manual). Cheers, Tsjerk On 11/10/08, Alessandro Casoni [EMAIL PROTECTED] wrote: Hi all, when i use editconf to generate a dodecahedron box with the command: editconf -f protein.gro -bt dodecahedron -o box.gro -d 0.9 the output show me the following message: . WARNING 1 [file aminoacids.dat, line 1]: Bad box in file protein.gro Generated a cubic box6.941 x4.939 x7.460 . what is the mean of bad box in file? and why editconf generates a cubic box? I use gromacs 4.0 regards, Alessandro ___ 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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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] Gromacs-4.0.2 is out
Hi, I think we've fixed all minor issues with Gromacs-4.0 now; please download the new release from ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.0.2.tar.gz Now, a friend of order might ask what happened to 4.0.1 that appeared on the ftp site for a couple of hours on friday? Unfortunately we accidentally disabled all water optimization in that brown-paper-bag-over-head release, which will result in a serious performance drop. Thus, PLEASE UPGRADE TO 4.0.2 ASAP IF YOU INSTALLED 4.0.1! Sorry for the confusion - now that we have a somewhat stable release we'll concentrate on creating binary packages! Cheers, Erik ___ 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] Re: gmx-users Digest, Vol 55, Issue 51
I have checked the source code and it looks like g_spatial has been replaced by
g_cluster.I got the code below under g_spatial.c
/* This is just a wrapper binary.
* The code that used to be in g_cluster.c is now in gmx_cluster.c,
* where the old main function is called gmx_cluster().
*/
int
main(int argc, char *argv[])
{
gmx_cluster(argc,argv);
return 0;
}
Gadzikano
-- original message --
I am not sure what is going on in this case. You could try:
which g_spatial
to see what is being picked up. You could also try to move the
g_spatial executable to its own directory and then execute g_spatial
from that path:
/new/path/to/executable/g_spatial -h
ls /new/path/to/executable/g_spatial
g_spatial
Otherwise I am not sure what is going on. Are you sure that you didn't
compile g_cluster under the name g_spatial by accident?
Chris.
-- original message --
HI Chris
I followed the steps below and when i tried to run g_spatial it
executed g_cluster instead. Even when i do g_spatial -h it looks like
its being overwritten by g_cluster
1.I used make_ndx to create a group containing the atoms around which i want
the SDF
2. trjconv -s md.tpr -f tyrc_md.trr -o tyrc1.xtc -center tric -ur
compact -pbc none
3. trjconv -s md.tpr -f tyrc1.xtc -o tyrc2.xtc -fit rot+trans
4. g_spatial -s md.tpr -f tyrc2.xtc -n index.ndx
--
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[gmx-users] files to modify to add NH2 cap at C terminal end
Hi everyone, I had asked this question before but I will try to explain myself more clearly. I wan t to add -NH2 cap at the Cterminal end of my protein. I had included charmm force field into my gromacs 3.3.1. I had added the following into my ffcharmm-c.tdb file [NH2] [replace] O OB 15.994 -0.550 CACT112.0110 0.070 C CD 12.0110 0.720 [add] 1 4NH2 C CA C NH2 14.0027 -0.7800 2 3HT N CA C HT 1.0080 0.3100 However, the coordinates of the added N is given by pdb2gmx as nan nan nan. If anyone can give any suggestion to fix this poblem, I will be highly obliged. Thanks in advance, Sarbani ___ 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
Re: [gmx-users] Gromacs-4.0.2 is out
Great job! Around when will the manual be ready? Regards, Suman Chakrabarty. Erik Lindahl wrote: Hi, I think we've fixed all minor issues with Gromacs-4.0 now; please download the new release from ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.0.2.tar.gz Now, a friend of order might ask what happened to 4.0.1 that appeared on the ftp site for a couple of hours on friday? Unfortunately we accidentally disabled all water optimization in that brown-paper-bag-over-head release, which will result in a serious performance drop. Thus, PLEASE UPGRADE TO 4.0.2 ASAP IF YOU INSTALLED 4.0.1! Sorry for the confusion - now that we have a somewhat stable release we'll concentrate on creating binary packages! Cheers, Erik -- 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://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] .mdp file
Hello there, I have a practical question regarding the mdp file, regardless the system to simulate. Before I would run a md simulation, usually we have to run grompp in order to preprocess the system. So I obtain, among other files, the mdout.mdp, based on the input mdp file. My question: If I want to run another simulation, with the same input, only with small changes in the mdp file (like number of steps or so), do I have to each time modify the input .mdp and run grompp, or is it enough if I modify mdout.mdp? Best regards, Andrea ___ 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] Re: Spatial distibution
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individual capacity.
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---BeginMessage---
I have checked the source code and it looks like g_spatial has been replaced by
g_cluster.I got the code below under g_spatial.c
/* This is just a wrapper binary.
* The code that used to be in g_cluster.c is now in gmx_cluster.c,
* where the old main function is called gmx_cluster().
*/
int
main(int argc, char *argv[])
{
gmx_cluster(argc,argv);
return 0;
}
Gadzikano
-- original message --
I am not sure what is going on in this case. You could try:
which g_spatial
to see what is being picked up. You could also try to move the
g_spatial executable to its own directory and then execute g_spatial
from that path:
/new/path/to/executable/g_spatial -h
ls /new/path/to/executable/g_spatial
g_spatial
Otherwise I am not sure what is going on. Are you sure that you didn't
compile g_cluster under the name g_spatial by accident?
Chris.
-- original message --
HI Chris
I followed the steps below and when i tried to run g_spatial it
executed g_cluster instead. Even when i do g_spatial -h it looks like
its being overwritten by g_cluster
1.I used make_ndx to create a group containing the atoms around which i want
the SDF
2. trjconv -s md.tpr -f tyrc_md.trr -o tyrc1.xtc -center tric -ur
compact -pbc none
3. trjconv -s md.tpr -f tyrc1.xtc -o tyrc2.xtc -fit rot+trans
4. g_spatial -s md.tpr -f tyrc2.xtc -n index.ndx
--
---End Message---
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Re: [gmx-users] g_rms
Hi Tatsiana, No. g_rms requires the input trajectory and the reference structure to match. Actually, the trajectory (if .xtc format) does not even contain information regarding the atoms; only coordinates. Tools depend wholly on the reference structure for information on atom/residue names, etc. Cheers, Tsjerk On Mon, Nov 10, 2008 at 5:36 PM, Tatsiana Kirys [EMAIL PROTECTED] wrote: Hi, i use g_rms to calculate rms, as reference structure (-s) i use myprotein.pdb file and trajectory (-f) is a trajectiry after MD MDprotein.pdb. The thing is that myprotein.pdb and MDprotein.pdb have the same atoms BUT their order within a residue is DIFFERENT. example: myprotein.pdb: ATOM 1 N ALA E 1 18.858 -22.883 26.306 1.00 0.00 ATOM 2 CA ALA E 1 19.106 -24.277 26.027 1.00 0.00 ATOM 3 C ALA E 1 20.206 -24.458 25.006 1.00 0.00 ATOM 4 O ALA E 1 20.156 -23.801 23.972 1.00 0.00 ATOM 5 CB ALA E 1 17.865 -24.819 25.301 1.00 0.00 MDprotein.pdb: ATOM 1 N ALA 1 18.861 24.179 26.290 1.00 0.00 ATOM 2 CA ALA 1 18.978 22.741 26.011 1.00 0.00 ATOM 3 CB ALA 1 17.670 22.190 25.440 1.00 0.00 ATOM 4 C ALA 1 20.069 22.592 24.949 1.00 0.00 ATOM 5 O ALA 1 20.120 23.450 24.070 1.00 0.00 whether g_rms work correct in this case? g_rms -s myprotein.pdb -f MDprotein.pdb ___ 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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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
Re: [gmx-users] Deuterium order parameter over area of membrane
On Mon, 10 Nov 2008 11:09:01 +0530 anirban polley [EMAIL PROTECTED] wrote: Hi, I know that deuterium order parameter can be calculated by g_density but it calculate average deuterium order parameter of a type of lipid Vs. atom number of the tail of the lipid. But I want to calculate deuterium order parameter fluctuation over the area. i.e., I want to know to calculate Scd per area of the membrane. Could you tell me how to do it. You may want to generate an index that would give the lipids in the area you are interested in. This would work for the thickness, the density and S_CD. You'll need to make the index by a script of your own as make_ndx does not select based on positions bu only on names etc. It is not difficult anyways. XAvier. Thanks, Anirban ___ 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 - XAvier Periole - PhD - Molecular Dynamics Group - Computation and NMR University of Groningen The Netherlands - ___ 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
Re: [gmx-users] .mdp file
Andrea Muntean wrote: Hello there, I have a practical question regarding the mdp file, regardless the system to simulate. Before I would run a md simulation, usually we have to run grompp in order to preprocess the system. So I obtain, among other files, the mdout.mdp, based on the input mdp file. My question: If I want to run another simulation, with the same input, only with small changes in the mdp file (like number of steps or so), do I have to each time modify the input .mdp and run grompp, or is it enough if I modify mdout.mdp? No. The mdout.mdp file is output, a record of all the simulation parameters, including the ones you accepted as defaults by not explicitly entering into your grompp.mdp file (the input). If you want to run different simulations, you need to modify your input, or else these new parameters will never reach the .tpr file and you will be running the same thing over and over again. -Justin Best regards, Andrea ___ 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 -- Justin A. Lemkul Graduate Research Assistant 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://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
Re: [gmx-users] bad box in protein.gro
Tsjerk Wassenaar ha scritto: Hi Alessandro, editconf encounters a bad box in the input file and I think it first replaces that with a standard box internally. Check the box at the end of box.gro to see if the result is what it should be (nine numbers, according to the specification of the rhombic dodecahedon in Chapter 3 of the manual). Cheers, Tsjerk On 11/10/08, Alessandro Casoni [EMAIL PROTECTED] wrote: Hi all, when i use editconf to generate a dodecahedron box with the command: editconf -f protein.gro -bt dodecahedron -o box.gro -d 0.9 the output show me the following message: . WARNING 1 [file aminoacids.dat, line 1]: Bad box in file protein.gro Generated a cubic box6.941 x4.939 x7.460 . what is the mean of bad box in file? and why editconf generates a cubic box? I use gromacs 4.0 regards, Alessandro ___ 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 Thank you Tsjerk, i appreciate your help..if i copy the last line at the end of box.gro in my protein.gro and rerun the editconf command i obtain: Volume: 729.043 nm^3, corresponds to roughly 328000 electrons No velocities found system size : 6.941 4.939 7.459 (nm) diameter: 8.302 (nm) center : -1.289 -0.528 4.099 (nm) box vectors : 10.102 10.102 10.102 (nm) box angles : 60.00 60.00 90.00 (degrees) box volume : 729.04 (nm^3) shift : 8.866 8.105 -0.528 (nm) new center : 7.577 7.577 3.572 (nm) new box vectors : 10.102 10.102 10.102 (nm) new box angles : 60.00 60.00 90.00 (degrees) new box volume : 729.04 (nm^3) and the bad box message disappears.. Ale ___ 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] the Temperature in the mdp.file
Hi all users. When I change the Temperature in the madp file to try to get different result about DNA model's disassociation , but it is strange that result seems to be the same for different Temperature. Even I change the Temperature by 0K ,the disassociation happened. I have tried to reduce the force between some bond and non-bond, but the effect is not very good. This is part of my mdp file: ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.0001 nsteps =10 ; For exact run continuation or redoing part of a run init_step= 0 ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 10 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xyz ; nblist cut-off rlist= 0.686 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = User rcoulomb-switch = 0 rcoulomb = 0.9 ; Relative dielectric constant for the Cut-off or DC of the reaction field epsilon-r= 78 ; Method for doing Van der Waals vdw-type = User ; cut-off lengths rvdw-switch = 0 rvdw = 0.9 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Seperate tables between energy group pairs energygrp_table = ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii = 2 ; Salt concentration in M for Generalized Born models gb_saltconc = 0 ; IMPLICIT SOLVENT (for use with Generalized Born electrostatics) implicit_solvent = No ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = berendsen ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau_t= 0.1 ref_t= 300 ; Pressure coupling Pcoupl = no Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p= 0.5 compressibility = 4.5e-5 ref_p= 1.0 ; Random seed for Andersen thermostat andersen_seed= 815131 Can anyone of you tell me what is the reason for that? Thank you in advance. Yang ___ 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
Re: [gmx-users] the Temperature in the mdp.file
Is it a real diassociation or an illusion? Visualize with PBC in mind. To put them back, use trjconv to center one chain of the DNA and output the two chains. On 11/11/08, He, Yang [EMAIL PROTECTED] wrote: Hi all users. When I change the Temperature in the madp file to try to get different result about DNA model\'s disassociation , but it is strange that result seems to be the same for different Temperature. Even I change the Temperature by 0K ,the disassociation happened. I have tried to reduce the force between some bond and non-bond, but the effect is not very good. This is part of my mdp file: ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.0001 nsteps =10 ; For exact run continuation or redoing part of a run init_step= 0 ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 10 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xyz ; nblist cut-off rlist= 0.686 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = User rcoulomb-switch = 0 rcoulomb = 0.9 ; Relative dielectric constant for the Cut-off or DC of the reaction field epsilon-r= 78 ; Method for doing Van der Waals vdw-type = User ; cut-off lengths rvdw-switch = 0 rvdw = 0.9 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Seperate tables between energy group pairs energygrp_table = ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii = 2 ; Salt concentration in M for Generalized Born models gb_saltconc = 0 ; IMPLICIT SOLVENT (for use with Generalized Born electrostatics) implicit_solvent = No ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = berendsen ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau_t= 0.1 ref_t= 300 ; Pressure coupling Pcoupl = no Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p= 0.5 compressibility = 4.5e-5 ref_p= 1.0 ; Random seed for Andersen thermostat andersen_seed= 815131 Can anyone of you tell me what is the reason for that? Thank you in advance. Yang ___ 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 -- Regards, Yang Ye ___ 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] gro file
hello everyone, i m having a peptide of 3 residue named Boc-BetaAla-Aib-OMe made from prodrg server when i give the grompp command for vacuum i.e. grompp -f boc1_vac_st.mdp -c boc1.gro -p boc1.top -o boc1_vac_st.tpr i got an error: ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rlist. i have set my rlist=0.8 and rvdw=0.7. In my gro file i m having X, Y, Z coordinates which - 1.41000 1.41000 1.41000 so i increase my X, Y, Z coordinates to - 1.65000 1.65000 1.65000 then i get no error. tell me whether i m correct at this point. or Shd i decrease my rlist and rvdw with regards Bhawana ___ 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
Re: [gmx-users] gro file
Bhawana Gupta wrote: hello everyone, i m having a peptide of 3 residue named Boc-BetaAla-Aib-OMe made from prodrg server when i give the grompp command for vacuum i.e. grompp -f boc1_vac_st.mdp -c boc1.gro -p boc1.top -o boc1_vac_st.tpr i got an error: ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rlist. i have set my rlist=0.8 and rvdw=0.7. In my gro file i m having X, Y, Z coordinates which - 1.41000 1.41000 1.41000 so i increase my X, Y, Z coordinates to - 1.65000 1.65000 1.65000 then i get no error. So your cutoff is now consistent with your box size. tell me whether i m correct at this point. or Shd i decrease my rlist and rvdw There've been posts on this in the last week or two. rvdw and rcoulomb should not be varied much (or at all) from whatever they were when the force field was parameterized, otherwise your physics is garbage. At the moment your .tpr describes a numerical procedure that is well-enough formed to give to mdrun. Whether it will explode or produce a useful result depends on all the other decisions you've made. Since you haven't said what you're trying to do with this peptide, we really can't assess whether you're correct. It's also not our job to do so... We didn't get our knowledge and judgement magically, we got it from doing lots of reading and experimentation. You'll learn better if you do likewise. Mark ___ 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] replicating a view in pymol for multiple files
Hi There, My apologies to ask a question not related to gromacs here. I want to know how can I generate a particular view in PYMOL ? like if I am having around 50 pdb files and I want to visualize them all in a particular view (giving differetnt color to different residue,,etc) Can I do it by writing a script or so. Please guide me for te same.. with thanks, Vivek ___ 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
Re: [gmx-users] questions in Running MDS over docked poses
hi Justin, Thanks for your reply... I am interested in looking for the stability of the docked pose, by applying some temperature variation in the molecule. If I am applying temperature variation then should I use pressure coupling simultaneously. Can you suggest some tutorial for such attempts. With Thanks, Vivek 2008/11/10 Justin A. Lemkul [EMAIL PROTECTED] vivek sharma wrote: Hi There, I am running MDS over the docked poses to check the stability of the docked poses using gromacs. I have few doubts about selecting parameters for the same, If anybody have tried such thing earlier, please suggest me for the same. Should I keep pressure coupling over the simulation ? Sure; life exists at NPT, so it is commonly used in routine protein simulations. For how long should I run the simulation for such purpose ? That's up to you :) You should run the simulations as long as you feel necessary to achieve stability. I know that's vague, but there really is no single correct answer to this question in the MD field. If there is, I'd love for someone to tell me, too...;) -Justin Waiting for suggestions. With Thanks, Vivek ___ 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 -- Justin A. Lemkul Graduate Research Assistant 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://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 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
Re: [gmx-users] replicating a view in pymol for multiple files
vivek sharma wrote: Hi There, My apologies to ask a question not related to gromacs here. I want to know how can I generate a particular view in PYMOL ? like if I am having around 50 pdb files and I want to visualize them all in a particular view (giving differetnt color to different residue,,etc) Can I do it by writing a script or so. You might be better served asking such a question on a Pymol list. For the record, I expect VMD will also be able to use scripting to achieve such a task. Mark ___ 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
RE: [gmx-users] freeze group gives Segmentation fault
Hi, I don't understand your mail. Do you really get a segmentation fault, but also frames in your trajectory file? I think I fixed the freezing of the whole system bug. I tested it for a water system and it runs fine. Maybe you have constraints in your system. Asking your system to be completely frozen and to obey the constraints is usually contradictory. Therefore you system might still move slightly to try to obey the constraints. Anyhow it seems pretty useless to me to simulate a completely frozen system. Berk From: [EMAIL PROTECTED] Date: Mon, 10 Nov 2008 15:13:06 +0100 To: gmx-users@gromacs.org Subject: Re: [gmx-users] freeze group gives Segmentation fault I just tried Gromacs 4.0.2. It still gives a Segmentation fault: Reading file topol.tpr, VERSION 4.0.2 (single precision) Loaded with Money Segmentation fault I did a test, putting the whole system into one freezegroup. Then the simulation starts running. But some of the atoms belonging to the freeze-group still move: The RMSD keeps growing and the Potential Energy = -132 kJ/mol. Reading in the trajectory with vmd shows the molecules moving. There is no pattern in the motion though. I checked the index.ndx twice - there is no mistake in there. Ilona There was a bug in the freeze group code that got fixed today. I don't know anything else about it. Please update your source code and try again. Mark [EMAIL PROTECTED] wrote: Using freezegroups I get a Segmentation fault. The simulation does not start, so the output is empty. Reading file topol.tpr, VERSION 4.0_rc4 (single precision) Segmentation fault _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ 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
