Re: [gmx-users] Can not open file: traj.xtc
Did you set the -f parameter to point to the right file? Never used g_rotacf, but traj.xtc is the default file name for the trajectory file. // Linus On Sun, Feb 17, 2013 at 12:57 PM, Sabrina Kemmerer wrote: > Hi, > > I copied the output files of my simulation on another computer and tried to > run g_rotacf. > I already did the same calculation on the other computer using the same > version of Gromacs. > Everything worked fine there, but now I get the error message 'Can not open > file: traj.xtc'. > I checked if the file was copied correctly by calculating the md5 sums. > VMD is also able to load frames from the file. > > Can anyone help me to fix this problem? > > > Best regards, > Sabrina > > ERROR message: > > > Program g_rotacf, VERSION 4.5.4 > Source code file: > /pathtogromacssource/Gromacs4.5.4-src/gromacs-4.5.4/src/gmxlib/gmxfio.c, > line: 519 > > Can not open file: > traj.xtc > -- > 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] About system requirement to gromacs
Both are probably using 4 cores, the first one as threads, the second via mpi. However, in the second one you are using 16 threads to run 4 copies of the same simulation, 4 threads each, thus getting performance similar (or less) to using only one core. When using mpi, you should use mdrun_mpi instead, ie: mpirun -np 4 mdrun_mpi -v -deffnm topol1 / Linus On Wed, Aug 1, 2012 at 12:36 PM, rama david wrote: > Thank you Mark for reply.. > > I run mdrun and mpirun with following command. I pasted output also.. > Please help me to parse it.. > > > 1. mdrun -v -deffnm topol1 > 2. mpirun -np 4 mdrun -v -deffnm topol1 > > > 1.mdrun -v -deffnm topol1 > > > step 30, will finish Wed Aug 1 16:49:28 2012 > Average load imbalance: 12.3 % > Part of the total run time spent waiting due to load imbalance: 5.1 % > > NOTE: 5.1 % performance was lost due to load imbalance > in the domain decomposition. > You might want to use dynamic load balancing (option -dlb.) > > > Parallel run - timing based on wallclock. > >NODE (s) Real (s) (%) >Time: 2.035 2.035100.0 >(Mnbf/s) (GFlops) (ns/day) (hour/ns) > Performance:109.127 5.744 2.632 9.117 > > gcq#98: "You're About to Hurt Somebody" (Jazzy Jeff) > > > > 2. mpirun -np 4 mdrun -v -deffnm topol1 > > Getting Loaded... > Reading file topol1.tpr, VERSION 4.5.5 (single precision) > Starting 4 threads > Starting 4 threads > Starting 4 threads > Starting 4 threads > Loaded with Money > > Loaded with Money > > Loaded with Money > > Loaded with Money > > Making 1D domain decomposition 4 x 1 x 1 > Making 1D domain decomposition 4 x 1 x 1 > > > Making 1D domain decomposition 4 x 1 x 1 > Making 1D domain decomposition 4 x 1 x 1 > > starting mdrun 'Protein in water' > 5 steps,100.0 ps. > starting mdrun 'Protein in water' > 5 steps,100.0 ps. > > starting mdrun 'Protein in water' > 5 steps,100.0 ps. > starting mdrun 'Protein in water' > 5 steps,100.0 ps. > > NOTE: Turning on dynamic load balancing > > > NOTE: Turning on dynamic load balancing > > step 0 > NOTE: Turning on dynamic load balancing > > step 100, will finish Wed Aug 1 19:36:10 2012vol 0.83 imb F 2% vol > 0.84 imb step 200, will finish Wed Aug 1 19:32:37 2012vol 0.87 imb > F 16% vol 0.86 imb step 300, will finish Wed Aug 1 19:34:59 2012vol > 0.88 imb F 4% vol 0.85 imb step 400, will finish Wed Aug 1 > 19:36:27 2012^Cmpirun: killing job... > > -- > mpirun noticed that process rank 0 with PID 4257 on node VPCEB34EN > exited on signal 0 (Unknown signal 0). > -- > 4 total processes killed (some possibly by mpirun during cleanup) > mpirun: clean termination accomplished > > > > > As you can also see the mdun command estimate to complete Aug 1 16:49:28 2012 > while mpirun taking the time Wed Aug 1 19:36:10 2012vol > > Mpirun command taking more time... > > so from above output I can guess In mpirun 4 processor are used > > > Sorry if I take any wrong meaning from output.. > > Thank you for giving your valuable time.. > > > With best wishes and regards > > Rama David > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * 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 * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Gromacs installation
If you install package 1 on your list, the second one will be installed as well (ie you need both of them). // Linus On Mon, Jul 30, 2012 at 10:56 AM, rama david wrote: > Hi GROMACS FRIENDS, > I have dell T3500 precision, 64 bits, 6C workstation with fedora > operating system. > I want to install gromacs in parallel mode with mpi... > I am planning to performed Replica Exchange Molecular Dynamics ( REMD ). > As per REMD instruction > http://www.gromacs.org/Documentation/How-tos/REMD?highlight=remd, > GROMACS should not compile in threading. > I install open mpi with command line yum -y install openmpi. > I found that fedora add/remove software package has gromacs 4.5.5 > version that can be > easily installed by command yum .. > It enlisted with total 15 different packages : eg.. two packages.. > > 1. GROMACS Open MPI binaries and libraries > 2 . GROMACS OPEN MPI shared libraries > > and a more.. > > Please can you tell me which packages I have to install so that I can > run GROMACS 4.5.5 in parallel to do REMD. > > > Thank you in advance > Have a nice day.. > > > With Best Wishes and regards. > Rama David > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * 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 * Only plain text messages are allowed! * 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: question about minimisation
Quite sure it's just different syntax in topology and mdp file. Compare to C; #define POSRES // expressed as -DPOSRES in the mdp file #ifdef POSRES // when working in the topology file // Linus On Thu, Jul 26, 2012 at 1:52 PM, wrote: >> >> >> On 7/26/12 7:06 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: On 7/26/12 6:07 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: >> On 26/07/2012 6:47 PM, reising...@rostlab.informatik.tu-muenchen.de >> wrote: >>> Ho, >>> first I minimize my structure. This is the corresponding mdp file: >>> >>> define = -DPOSRES >>> integrator = steep >>> emtol = 10 >>> nsteps = 1500 >>> nstenergy = 1 >>> energygrps = System >>> coulombtype = PME >>> rcoulomb= 0.9 >>> rvdw= 0.9 >>> rlist = 0.9 >>> fourierspacing = 0.12 >>> pme_order = 4 >>> ewald_rtol = 1e-5 >>> pbc = xyz >>> >>> >>> and then I run a md run. This is the corresponding mdp file: >>> >>> define = -DPOSRES >>> integrator = md >>> dt = 0.001 >>> nsteps = 5000 >>> nstxout = 100 >>> nstvout = 0 >>> nstfout = 0 >>> nstlog = 1000 >>> nstxtcout = 500 >>> nstenergy = 5 >>> energygrps = Protein Non-Protein >>> nstcalcenergy = 5 >>> nstlist = 10 >>> ns-type = Grid >>> pbc = xyz >>> rlist = 0.9 >>> coulombtype = PME >>> rcoulomb= 0.9 >>> rvdw= 0.9 >>> fourierspacing = 0.12 >>> pme_order = 4 >>> ewald_rtol = 1e-5 >>> gen_vel = yes >>> gen_temp= 200.0 >>> gen_seed= >>> constraints = all-bonds >>> tcoupl = V-rescale >>> tc-grps = Protein Non-Protein >>> tau_t = 0.1 0.1 >>> ref_t = 298 298 >>> pcoupl = no >>> >>> >>> >>> In my topology file I include the restraint files like this: >>> >>> ; Include Position restraint file >>> #ifdef POSRES >>> #include "posre.itp" >>> #endif >>> >>> #ifdef POSRES >>> #include "posre_memb.itp" >>> #endif >> >> This won't work for multiple [moleculetype] entries. See >> http://www.gromacs.org/Documentation/How-tos/Position_Restraints >> >>> >>> >>> I just recognize that there is a "DPOSRES" in the mdp files and a >>> "POSRES" >>> in my topology file. Is this the problem. Do I have to write it the >>> same >>> way in the several files? >> >> http://www.gromacs.org/Documentation/Include_File_Mechanism >> >> Mark > > > I just see that the [ position_restraints ] part is included under the > [dihedral] and not between the [moleculetype] and the [atom] part. And > according to the site you wrote me this is a problem, right? But this > was > done by gromacs itself. Shell I write it to the [moleculetype] part? > A [position_restraints] directive belongs to the [moleculetype] in which it is declared. The original location of the #include statement produced by Gromacs is correct; it follows sequentially within the protein [moleculetype]. Your inclusion of the membrane restraint file within the protein [moleculetype] is, however, incorrect. > But I can not see why it can not work that I have 2 restriction files? > Can > you please explain it to me? > You can have two restraint files for different [moleculetypes] but they must be organized as such. >>> >>> okey. So the whole thing with [atoms], [bonds], [dihedral] all contains >>> to >>> the entry in [moleculetype] , right? >>> >> >> Any directive belongs to the [moleculetype] that immediately precedes it. >> Once >> a new [moleculetype] is declared (either directly or indirectly via >> #include >> mechanism), you're working with a different molecule. >> >>> But directly before I include the membrane restriction file I include >>> the >>> membrane definition: >>> >>> #include "amber03.ff/dum.itp" >>> #ifdef POSRES >>> #include "posre_memb.itp" >>> #endif >>> >>> >>> So I thought that it is directly after the atomtype it belongs to. I >>> thought that it is the same in the case with the water, where first the >>> water definition is included and after that the restriction of the >>> water. >>> >>> Or am I wrong? >>> >> >> Well the #include statement shown here is different than the one you >> showed >> previously, which was wrong. Please alwa
Re: [gmx-users] MPIRUN on Ubontu
In order to use MPI on Ubuntu with the distribution-supplied package, you need to use a combination of mpirun and mdrun_mpi, e.g. mpirun -np 2 mdrun_mpi -deffnm md to run on two cores. On Mon, Dec 27, 2010 at 7:04 PM, Justin A. Lemkul wrote: > > > גדעון לפידות wrote: >> >> Hi all, >> I have recently installed Ubonto on my computer (i5 processor) and >> installed gromacs 4.0.7. I have installed openmpi and fftw but when using >> mpirun command instead of getting parallel processes it simply runs the same >> job four times simultaneously. How do I make the necessary adjustments. > > Properly compile an MPI-enabled mdrun. Since you've provided no detail on > how you did the installation, the only thing to suggest is that you've done > something wrong. Follow the installation guide: > > http://www.gromacs.org/Downloads/Installation_Instructions > > Alternatively, use the newest version of Gromacs (4.5.3), which uses > threading for parallelization instead of requiring external MPI support. > > -Justin > >> Thanks, >> Gideon >> > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing list gmx-us...@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] what is the "nicelevel" ?
The nicelevel is simply the priority of the process, where 19 is the lowest priority (ie most other programs will use the cpu before the gromacs process does) and -20 the highest. See man nice. // Linus On Tue, Dec 7, 2010 at 10:13 PM, GZ Zhang wrote: > Hi, ALL > I'm using "genbox" to create a water box. There is a flag called > "-nice" which is described to be used to set the nicelevel. > What is nicelevel ? What does the default value "19" mean ? What if I would > like to increase the decimal places (the default > is 3) of all numbers. Thanks. > Regards, > Guozhen > > -- > gmx-users mailing list gmx-us...@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] dssp
What did you try to do? To use dssp, you must select entire residues, e.g. 1 (protein). That error sounds a bit like my problem when trying to do dssp using only the backbone. // Linus Östberg On Fri, Nov 5, 2010 at 2:08 PM, #ZHAO LINA# wrote: > Hi, > > Thanks for your response, I modified that path parts when I posted that > information. > > So my environment set was correct. > > I just suddenly realize I may not have root privilege there, cause the dssp > was not small, not in mine personal computer, there are in some other places. > > lina > > > From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf > of Justin A. Lemkul [jalem...@vt.edu] > Sent: Friday, November 05, 2010 9:07 PM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] dssp > > #ZHAO LINA# wrote: >> Hi, >> >> Program do_dssp, VERSION 4.0.7 >> Source code file: pathToGromacs/gromacs-4.0.7/src/tools/do_dssp.c, line: 471 >> >> Fatal error: >> Failed to execute command: pathToDSSP/ -na ddEPI6I2 ddFHouPz > /dev/null >> 2> /dev/null >> >> It came out two or three file like ddEPI6I2 and then died like above. >> >> My first time try dssp, so do not know how to examine it. >> > > Your DSSP environment variable is set incorrectly. do_dssp is trying to call > "pathToDSSP" as the executable. > > http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp > > Note that you should substitute a meaningful PATH on your system, not > something > like "pathToDSSP." > > -Justin > >> Thanks for any advice, >> >> lina >> > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing list gmx-us...@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 list gmx-us...@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 subject)
Use grompp normally, without the -np flag. Then run mdrun_mpi with your normal parameters as mpirun -np x mdrun_mpi -deffnm xx On Mon, Jun 21, 2010 at 2:00 PM, Amin Arabbagheri wrote: > Hi all, > > I've installed GROMACS 4.0.7 and MPI libraries using ubuntu synaptic > package manager. > I want to run a simulation in parallel on a multi processor, single PC, but > to compile via grompp, it doesn't accept -np flag, and also , using -np in > mdrun, it still runs as a single job. > Thanks a lot for any instruction. > > Bests, > Amin > > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
