Re: [gmx-users] General Questions about Molecular Dynamics

bad results. -- Mr. Jussi Lehtola, M. Sc. Doctoral Student jussi.leht...@helsinki.fi Department of Physics http://www.helsinki.fi/~jzlehtol University of Helsinki Office phone: +358 9 191 50 632 Finland

Re: [gmx-users] About MD

would set p=0=T. -- Mr. Jussi Lehtola, M. Sc. Doctoral Student jussi.leht...@helsinki.fi Department of Physics http://www.helsinki.fi/~jzlehtol University of Helsinki Office phone: +358 9 191 50 632 Finland

Re: [gmx-users] gromacs: sound wave in liquid?

this. Not to mention the time scales - in order to simulate a sound wave say, at 44 kHz, you'd need to get at least two periods in your simulations, i.e. 45 microseconds, which is a *long* time on the nuclear / MD timescale. -- Mr. Jussi Lehtola, M

Re: [gmx-users] xmgrace

/epel/5/i386/epel-release-5-4.noarch.rpm after which you can install grace with # yum -y install grace -- Mr. Jussi Lehtola, M. Sc. Doctoral Student jussi.leht...@helsinki.fi Department of Physics http://www.helsinki.fi

Re: [gmx-users] Comparing single with double precision runs

thermostats (or barostats), using double precision is mostly just a waste of resources, since the thermostat will just waste the extra precision. -- Mr. Jussi Lehtola, M. Sc. Doctoral Student jussi.leht...@helsinki.fi

Re: [gmx-users] Why does the -append option exist?

, independent processes all using the same trajectory file. Yes, this will probably lead to problems, unless the trajectory file is somehow locked. So: does GROMACS lock the trajectory files it operates upon? If not, it should. -- Mr. Jussi Lehtola, M

Re: [gmx-users] Slow Runs

a number out it doesn't mean that it's the right one... -- -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland jussi.leht...@helsinki.fi -- Jussi

Re: [gmx-users] Ubuntu Installation

fftw3f library What am I doing incorrectly? Looks like you're missing the development package. Run # apt-get install libfftw3-dev to fix this. -- -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki

Re: [gmx-users] Optimization of the box size during an energy minimization?

). -- -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland jussi.leht...@helsinki.fi -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht

Re: [gmx-users] simulation at constant temprature

or NPT, in which the system exchanges heat with a heat bath (NPT also has a pressure bath which tries to keep the pressure constant). -- -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland jussi.leht

[gmx-users] FYI: Fedora packages of Gromacs updated to 4.5.1

both thread and MPI parallelization so they should work fine on multiprocessor cluster systems. -- -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland jussi.leht...@helsinki.fi

Re: [gmx-users] Installation of gromacs on a cluster with gcc version 4.1.2

. The people at Red Hat have probably fixed all the bugs that caused the problems a long time ago. Another possibility is to ask the admin to install the 4.4 version of GCC, which is readily available in the distribution. -- -- Mr. Jussi Lehtola, M

Re: [gmx-users] Check V for NVT‏

Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland jussi.leht...@helsinki.fi

Re: [gmx-users] trying to install gromacs on linux single processor

is incorrect. To fix this, run # date [MMDDhhmm[[CC]YY][.ss] or, you can just fetch the time from a NTP server with # ntpdate 0.pool.ntp.org -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht

Re: [gmx-users] New beta release: 4.5-beta3

to the end of the flags, which causes a problem since the optimization settings are overruled. Plus, I think there should be some kind of minimal readme for usage with CMake. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin

Re: [gmx-users] New beta release: 4.5-beta3

+ GSL 1.14: GPLv3+ So, compiling Gromacs with GSL included results in a GPLv3+ binary. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632

Re: [gmx-users] mpi-run2

. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland

Re: [gmx-users] template.c

. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland jussi.leht

Re: [gmx-users] Compiling 4.0.7 parallel fails

MPI versions. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department

Re: [gmx-users] Compiling 4.0.7 parallel fails

. $ module load openmpi-x86_64 Furthermore, you should have the fftw-devel and openmpi-devel packages installed on your system. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191

Re: [gmx-users] Fwd: xmgrace

Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland jussi.leht...@helsinki.fi

Re: [gmx-users] gromacs 4.06 binary for linux -redhat

system and install fftw (system wide) with # yum -y install fftw-devel If you're interested, there's a binary package of Gromacs, too, available in EPEL, that you can install with # yum -y install gromacs -- -- Jussi Lehtola, FM

Re: [gmx-users] gromacs 4.06 binary for linux -redhat

On Thu, 2009-12-31 at 08:24 -0800, venkat wrote: I think I should be as root to do that. Yes, you must be root to install packages (unless you use rpm switches to redefine the root directory.) -- -- Jussi Lehtola, FM, Tohtorikoulutettava

[gmx-users] Pressure annealing in Gromacs?

structure quicker. Or are there any alternative ways to do this? -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 -- Mr

Re: [gmx-users] Pressure annealing in Gromacs?

change. Yes, this is of course what is probably happening. At least it would explain why the density is increasing so slowly after a temperature anneal to 1000 K. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto

Re: [gmx-users] Pressure annealing in Gromacs?

On Thu, 2009-12-03 at 02:30 +1100, Mark Abraham wrote: Jussi Lehtola wrote: I'm experiencing trouble converging the density of some heavy liquid alcohols (after 10 ns of simulation the density is still changing linearly). Is there any way to run pressure annealing in Gromacs? Running

Re: [gmx-users] LAM OpenMPI conflict?

, LAM has been obsoleted by Open MPI years ago, so you might just try switching from LAM to Open MPI, then you wouldn't have to run lamboot at the beginning.) -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht

Re: [gmx-users] LAM OpenMPI conflict?

on every MPI runtime. Your problem was with the Debian packages. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 -- Mr

Re: [gmx-users] Using gromacs 4.0.5 built with FORTIFY_SOURCE feature

? -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland jussi.leht

Re: [gmx-users] help needed for using xdr library

. Instead of #include xdrfile/xdrfile_xtc.h you need to use extern C { #include xdrfile/xdrfile.h } to get the name spaces correct. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p

Re: [gmx-users] help needed for using xdr library

On Mon, 2009-08-17 at 20:46 +0300, Jussi Lehtola wrote: you need to use extern C { #include xdrfile/xdrfile.h } Whoops, that should read extern C { -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto

Re: [gmx-users] Fwd: xdrfile library, read co-ordinates from .xtc

--disable-static --enable-shared compile and you end up with the shared library. Of course, you can compile the static version, too, if you want to. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht

Re: [gmx-users] GHrace install

.noarch.rpm and then install grace with # yum -y install grace Then you can run grace with $ xmgrace -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632

Re: [gmx-users] time of simulation

g_mdrun as the latter will just get you four independent processes that all perform the same calculation. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632

Re: [gmx-users] installing grace

the Fedora EPEL repo http://www.fedoraproject.org/wiki/EPEL/FAQ#howtouse and install grace with # yum -y install grace -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632

Re: [gmx-users] about template.c?

, to compile you need to add -I /path/to/gromacs/include -I /path/to/gromacs/include/types to the C compiler flags. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632

Re: [gmx-users] Buffer overflow on Fedora 10

you to install the debuginfo of other packages too. I have been working on getting also debug binaries in the package, but I won't push the new package until 4.0.6 is released which fixes the build error on ppc64 architecture. -- -- Jussi Lehtola

Re: [gmx-users] Buffer overflow on Fedora 10

: ../../../src/gmxlib/gmxfio.c, line: 736 Can not open file: topol.tpr (clip) Program exited with code 0377. Instead of running $ gdb g_mdrun [mdrun options] (gdb) run you need to run $ gdb g_mdrun (gdb) run [mdrun options] -- -- Jussi Lehtola

[gmx-users] Re: GMX-Installation2

installed, you have the single precision mpi version of mdrun as g_mdrun_mpi and double precision as g_mdrun_mpi_d. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632

Re: [gmx-users] GMX Installation

-devel gsl-devel lapack-devel and proceed with the Gromacs compilation. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 -- Mr

Re: [gmx-users] mpi mdrun

it need to open a file name \d hostfile and have a list for example like some thing below? If you're using openmpi on a quad core computer you just need to $ mpirun -np 4 mdrun_mpi (options) -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan

RE: [gmx-users] programmes to have in double precision besides mdrun_d

pathological cases than single precision. Still, usually it doesn't matter much whether the starting point was prepared in single or double precision. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht

Re: [gmx-users] problem in ngmx

everything is tunneled through SSH, it uses client-host authentication, works on every system, can be easily tunneled, can be compressed on slow connections (pass the -C option) and so on. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan

Re: [gmx-users] gromacs-4.0.5 parallel run in 8 cpu: slow speed

cpu showing 95-100% CPU. That's normal for a system that atoms/cpu ratio. What's your system and what mdp file are you using? -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632

Re: [gmx-users] Pressure and NVT Simulations

that the pressure can't be adjusted (it's done by scaling the simulation box), so having a negative pressure is normal. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632

Re: [gmx-users] Pressure and NVT Simulations

On Sat, 2009-06-06 at 00:30 +0530, Manik Mayur wrote: On Fri, Jun 5, 2009 at 11:58 PM, Jussi Lehtola jussi.leht...@helsinki.fi wrote: Generally speaking, if your density is too small, the system wants to increase it and thus you have negative pressure. If it is too

Re: [gmx-users] mdrun seems stuck

really is that slow. Switch to using coulombtype = PME, that should speed things up. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632

Re: [gmx-users] Shared library version binary on CYGWIN

and compiling with $ configure --enable-shared --disable-static after that. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632

Re: [gmx-users] Twin range cut-off's: rlist and rvdw

need to be as precise in taking those interactions into account. [1] http://dx.doi.org/10.1002/prot.340060203 -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632

Re: [gmx-users] Twin range cut-off's: rlist and rvdw

to r_cut^-4. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department

Re: [gmx-users] How to compile C++ propgram with xdrfile library?

. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics

[gmx-users] xdrfile license

that are GPL-licensed. Could someone please fix this? -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 -- Mr. Jussi Lehtola

Re: [gmx-users] positions and velocities of COM of whole water molecules instead of those of individual atoms?

don't publish your code then it may have any license whatever; if you publish it then it (as GROMACS) must be licensed under GPL. If there isn't a tool as such already available, it should be trivial to code. -- -- Jussi Lehtola, FM

Re: [gmx-users] Regarding the broken compiler gcc 4.1.x

of compilers still broken? because the message on gromacs download page is quite old. RedHat has backported a lot of fixes into their gcc, and thus the CentOS version works. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin

Re: [gmx-users] Timestep and force field

. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland jussi.leht

RE: [gmx-users] Cannot obtain the expected pressure using the Parrinello-Rahman coupling in a gas-liquid system

: 57 bar / 121 bar ~ 0.47 0.5 sigma. In x and y directions the deviation is even smaller: 85/201 ~ 0.42 -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632

Re: [gmx-users] Poor parallel performance in Ubuntu 8.04

this problem and solved it. That's highly unlikely: it would be a severe performance bug, which would have been picked up by the kernel packager. How did you configure the parallel version? What MPI environment did you use? -- -- Jussi Lehtola

Re: [gmx-users] Poor parallel performance in Ubuntu 8.04

On Wed, 2009-02-04 at 18:01 -0200, Alexandre Suman de Araujo wrote: Quoting Jussi Lehtola jussi.leht...@helsinki.fi: That's highly unlikely: it would be a severe performance bug, which would have been picked up by the kernel packager. How did you configure the parallel version? What MPI

Re: [gmx-users] installation problem

. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University

Re: [gmx-users] about the run program in gromacs 4.0.3

On Mon, 2009-01-26 at 10:54 +0100, XAvier Periole wrote: in the gmx-4.X versions you do not need to specify the number of CPU t grompp but only to mdrun ... Not mdrun, but to the MPI run program (mpirun / aprun c). -- -- Jussi Lehtola, FM

RE: Subject: Re: Re: [gmx-users] Gromacs 4 bug?

://cvs.fedoraproject.org/viewvc/devel/gromacs/gromacs.spec?view=log -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 -- Mr

[gmx-users] Equilibrating systems of rigid molecules

..? -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University

Re: [gmx-users] About 8 core CPUs platform

. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland jussi.leht...@helsinki.fi

Re: [gmx-users] Gromacs 4 with mpi interface

of a distributed one. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 -- Mr. Jussi Lehtola, M. Sc., Doctoral Student

Re: [gmx-users] Gromacs 4 with mpi interface

the MPI enabled analysis tools). Example: g_mdrun single precision g_mdrun_d double precision g_mdrun_mpi single precision MPI g_mdrun_mpi_d double precision MPI -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos

[gmx-users] Wrong manual on web page

Hi, the manual at ftp://ftp.gromacs.org/pub/manual/manual-4.0.pdf gives out the manual version 3.3, could somebody fix this? :) -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto [EMAIL PROTECTED], p. 191 50632

Re: [gmx-users] operating system

On Tue, 2008-11-18 at 13:49 +0530, Marudachalam S wrote: Hi, Thanks. What about RHEL? Will Gromacs run on it? Yes. You can even use the ready-compiled RPMs available from Fedora EPEL: Forwarded Message From: Jussi Lehtola [EMAIL PROTECTED] Reply-To: Discussion list

Re: [gmx-users] Gromacs Installation troubles

) g_mdrun_mpi (single precision, MPI) g_mdrun_mpi_d (double precision, MPI) You don't have to source GMXRC, it is done automatically. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto [EMAIL PROTECTED], p. 191 50632

Re: [gmx-users] Gromacs Installation troubles

/ Fedora EPEL + yum as I instructed a couple of mails ago. You should never use rpm's compiled for another distribution or architecture when you have native ones available. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin

Re: [gmx-users] Gromacs Installation troubles

it use the compiler options you want it to instead of manually compiling installing the software from the source tar files. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto [EMAIL PROTECTED], p. 191 50623

Re: [gmx-users] Gromacs Installation troubles

-- -- 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

Re: [gmx-users] Gromacs Installation troubles

to be automatically updated with yum, put the line exclude = gromacs* in /etc/yum.conf. When you want to update Gromacs to the newest version available, remove the line and run # yum -y update -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan

Re: [gmx-users] operating system

On Tue, 2008-11-18 at 12:19 +0530, Marudachalam S wrote: Hello, Can someone tell me if Gromacs will run on SuSe linux enterprise edition, with an AMD opteron processor? Yes, it will. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan

Re: [gmx-users] FFTW problem for Gromacs4

: # yum -y install gromacs for the serial version and # yum -y install gromacs-mpi for the parallel version. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto [EMAIL PROTECTED], p. 191 50623

Re: [gmx-users] Gromacs-4.0.2 is out

). 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

Re: [gmx-users] Re: High frequency output slow down the simulation?

simulations, since there is an extra communication step to collect the data. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto [EMAIL PROTECTED], p. 191 50623 -- Mr

Re: [gmx-users] Gromacs 4 SRC RPM?

/gromacs-4.0-3.fc9.src.rpm Or, if you have Fedora / RHEL, just use the compiled RPMS available from the mirror nearest to you. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto [EMAIL PROTECTED], p. 191 50632

[gmx-users] Fedora port of Gromacs available

gromacs-bash - bash autocompletion support gromacs-zsh - zsh support (GMXRC.zsh and autocompletion) gromacs-csh - csh support (GMXRC.csh and autocompletion in /usr/share/doc/gromacs-csh-4.0/doc) -- -- Jussi Lehtola, FM, Tohtorikoulutettava

[gmx-users] Binary compatibility Gromacs 3.x - 4.0

? -- -- 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

Re: [gmx-users] Binary compatibility Gromacs 3.x - 4.0

On Wed, 2008-10-08 at 17:27 +0200, David van der Spoel wrote: Jussi Lehtola wrote: Hi, are GROMACS 4.0 files binary compatible with GROMACS 3.(3.)x files? Explanation: I am working on a package of Gromacs 4 that is going to be included in Fedora. Is there still a need to have

Re: [gmx-users] Binary compatibility Gromacs 3.x - 4.0

clash with other packages. The solution is very likely environment modules. I'll send more info about the package when it's accepted. It will be available at least for RHEL 4, 5 and Fedora 9 and 10. -- -- Jussi Lehtola, FM, Tohtorikoulutettava

[gmx-users] Runtime CPU capabilities detection

... -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto [EMAIL PROTECTED], p. 191 50623 -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University

Re: [gmx-users] Threading in GROMACS

OpenMPI packages, in RHEL/Fedora install the packages openmpi{,-libs,-devel} and configure GROMACS with the MPI switch. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto [EMAIL PROTECTED], p. 191 50632

Re: [gmx-users] Time step in md

length constraints the time step is about 2 fs, if the molecules are flexible the time step needs to be a lot smaller, since hydrogen atoms oscillate very fast because of their small mass. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan

[gmx-users] OPLS atom types for THF simulations

topology I'd very much appreciate it. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto [EMAIL PROTECTED], p. 191 50632 -- Mr. Jussi Lehtola, M. Sc., Doctoral Student

Re: [gmx-users] OPLS atom types for THF simulations

. -- -- 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

Re: [gmx-users] Re: Installation gromacs

DO THIS WHEN GLIBC IS IN QUESTION! THIS IS GUARANTEED TO BREAK YOUR SYSTEM! The correct way is to rebuild Gromacs for your distribution. Either do the compilation manually or build a source RPM (SRPM) with rpmbuild. -- -- Jussi Lehtola, FM

Re: [gmx-users] simulations backward in time

. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto [EMAIL PROTECTED], p. 191 50673 -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki

Re: [gmx-users] instalation in FC7i386

libraries openmpi, fftw3 and so on. Try just with ./configure . If it doesn't work, then you might consider updating your OS to a supported version. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto [EMAIL PROTECTED

Re: [gmx-users] instalation in FC7i386

of weeks ago, so you should consider upgrading to a supported distribution.. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto [EMAIL PROTECTED], p. 191 50673 -- Mr

Re: [gmx-users] low cpu usage

(especially makewhatis, updatedb, prelink)? If you have a lot of I/O then you end up with a lot of wasted CPU time. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto [EMAIL PROTECTED], p. 191 50673

[gmx-users] Energy minimisation problem

coordinates topology -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto [EMAIL PROTECTED], p. 191 50673 -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department

RE: [gmx-users] Energy minimisation problem

topology it might give you clues, if something is wrong. Thanks, using the vacuum method I seem to get better results. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto [EMAIL PROTECTED], p. 191 50673

RE: [gmx-users] Energy minimisation problem

On Tue, 2008-05-13 at 20:32 +0300, Jussi Lehtola wrote: On Tue, 2008-05-13 at 14:34 +0100, Kukol, Andreas wrote: First try the EM/MD of 1 molecule in vacuum ('ethanol-gas') and check, if it looks reasonable. Thanks, using the vacuum method I seem to get better results. It seems I spoke

Re: [gmx-users] mpi.h is missing...

for Fortran 90). To run use grompp -np (number of processes) (normal args) to initialize and mpirun -np (number) mdrun -np (number) (args) Hope this solves your problem. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto

Re: [gmx-users] mpi.h is missing...

want to do also other MPI stuff than Gromacs, I recommend OpenMPI since it has Fortran 90 and full MPI 2 support. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto [EMAIL PROTECTED], p. 191 50673

[gmx-users] Question about x2top

-molecule topology made by x2top N times for a system of N molecules? -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto [EMAIL PROTECTED], p. 191 50673 -- Mr. Jussi

[gmx-users] Building simple alcohol topologies

seem to contain alcohols. I found some compounds from HIC-Ub, but for instance heptanol is missing. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto [EMAIL PROTECTED], p. 191 50673

[gmx-users] Building simple alcohol topologies

such files. If anyone could give me a few pointers on how and where to obtain these, I'd appreciate it a lot. -- -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland [EMAIL PROTECTED

[gmx-users] Dismantling the methyl group

and of the three hydrogens for the quantum mechanic computations. Is there any simple way to put the hydrogens in place using Gromacs, or do I need to program a way myself? -- Mr. Jussi Lehtola Research Assistant Division of Theoretical Physics / Division of High Energy Physics IT services Department

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