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

nstruct a seemingly sensible force field that ends up giving bad results. -- -------- Mr. Jussi Lehtola, M. Sc. Doctoral Student jussi.leht...@helsinki.fi Department of Physics http://www.helsinki.fi/~jzlehtol

Re: [gmx-users] About MD

ressure and V is volume. Here to minimize E you 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 Hel

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

7;d be somewhat skeptical about 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. -- -----------

Re: [gmx-users] xmgrace

wnload.fedoraproject.org/pub/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

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

that you are interested in. However, if you are using 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. D

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

ase where you have multiple, 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. -- ---------

Re: [gmx-users] Liquid/Gas Systems

T conditions, since gases > fill the volume of their container, right? NPT would indeed just > compress all of your particles together into a liquid. As I stated above, I'd say you can still have the "flying ice cube" effect in NVT. NPT won't compress the system into a

Re: [gmx-users] Slow Runs

t. Even if you get 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 --------

Re: [gmx-users] Ubuntu Installation

nnot find 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, Univ

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

tion in the Appendix). -- ---------- 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

Re: [gmx-users] simulation at constant temprature

hich 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

PI flavors have 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...@h

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

----- 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 Yliopi

Re: [gmx-users] Check V for NVT‏

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

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

said - your system clock time 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 Yliop

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

v2+, and 3 clause BSD => linking produces GPLv2+ GSL 1.14: GPLv3+ So, compiling Gromacs with GSL included results in a GPLv3+ binary. -- ------ Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Hel

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

-loops -O3 -DNDEBUG" is added 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, Toh

Re: [gmx-users] mpi-run2

te? The ones on the website are really old. -- ------ Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 ------ Mr. Jussi Lehtola, M. Sc., Doctoral Student Dep

Re: [gmx-users] template.c

s the same result. -- ---------- 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

Re: [gmx-users] Compiling 4.0.7 parallel fails

ROMACS; both in serial and in Open MPI versions. -- ---------- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 ---------- Mr. Jussi Leht

Re: [gmx-users] Compiling 4.0.7 parallel fails

edora 12, you need to load the MPI environment module with e.g. $ module load openmpi-x86_64 Furthermore, you should have the fftw-devel and openmpi-devel packages installed on your system. -- ------ Jussi Lehtola, FM, Tohtorikoulutettava F

Re: [gmx-users] Fwd: xmgrace

el-release-5-3.noarch.rpm # yum -y install grace -- ---------- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 ---------- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Phy

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,

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

on your 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 -- ------

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 pre

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

> a phase 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, Helsing

[gmx-users] Pressure annealing in Gromacs?

brium 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

Re: [gmx-users] LAM OpenMPI conflict?

nstallation. May be I don't > remember correctly. MPI is a standard so Gromacs works the same on every MPI runtime. Your problem was with the Debian packages. -- -- Jussi Lehtola, FM, Tohtorikoulutetta

Re: [gmx-users] LAM OpenMPI conflict?

our environment, which may quite well lead into problems. (Also, 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

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

4 and 5. Maybe your Gentoo is just broken? -- ------ Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 ------ Mr. Jussi Lehtola, M. Sc., Doctoral Student Department o

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 > } Whoops, that should read extern "C" { -- ---------- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsi

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

me? This is the result of non-matching name spaces. You're using C++, and xdrfile is written in C. Instead of #include you need to use extern C { #include } to get the name spaces correct. -- -- Jussi Lehtola, FM, Tohtorikoulutet

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

you just run $ ./configure --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, He

Re: [gmx-users] GHrace install

redhat.com/pub/epel/5/i386/epel-release-5-3.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 Yliopist

Re: [gmx-users] time of simulation

edora RPMs, you need to run $ mpirun -np 4 g_mdrun_mpi instead of $ mpirun -np 4 g_mdrun as the latter will just get you four independent processes that all perform the same calculation. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laito

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...@helsi

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

include "statutil.h" > #include "tpxio.h" > > what are they? > and, where are they? Those are GROMACS headers, to compile you need to add -I /path/to/gromacs/include -I /path/to/gromacs/include/types to the C compiler flags. --

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

] (gdb) run you need to run $ gdb g_mdrun (gdb) run [mdrun options] -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of

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

----- 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, Fi

[gmx-users] Re: GMX-Installation2

uffix. If you have gromacs-mpi 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...

Re: [gmx-users] GMX Installation

m -y install fftw-devel openmpi-devel gsl-devel lapack-devel and proceed with the Gromacs compilation. -- ------ Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@he

Re: [gmx-users] mpi mdrun

ost file? would 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,

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

y minimization since it can handle more 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 Fysi

Re: [gmx-users] problem in ngmx

-X server This way 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, Tohtorikoulut

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

while running all 8 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 Yliopis

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 > 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] Pressure and NVT Simulations

Now you are running NVT, meaning 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 Yliopis

Re: [gmx-users] mdrun seems stuck

the simulation 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

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

esulting in an error proportional to r_cut^-4. -- ---------- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 ---------- Mr. Jussi Lehtola, M.

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

n r>rlist the interactions are weaker and also vary more slowly, thus one doesn't need to be as precise in taking those interactions into account. [1] http://dx.doi.org/10.1002/prot.340060203 -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysii

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

ild scripts and updates libtool and compiling with $ configure --enable-shared --disable-static after that. -- ------ Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.le

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

can just use extern C { #include "xdrfile.h" #include "xdrfile_xtc.h" } int main() and so on The same thing also works for gromacs header files. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Ylio

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

you 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 Le

[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] Regarding the broken compiler gcc 4.1.x

tOS 4.3 and 5.0, both are obsolete: you should update to 4.7 and 5.3, respectively. > Are gcc 4.1.x series 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. -- -

Re: [gmx-users] Timestep and force field

me step is sufficiently small. -- ---------- 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

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

on compared to the fluctuations is small: 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 ju

Re: [gmx-users] obtaining gromacs for ubuntu (was Re: gmx-users Digest, Vol 58, Issue 125 (akalabya bissoyi))

is outdated). -- ------ 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] Poor parallel performance in Ubuntu 8.04

On Wed, 2009-02-04 at 18:01 -0200, Alexandre Suman de Araujo wrote: > Quoting Jussi Lehtola : > > 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 v

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

------ 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

Re: [gmx-users] installation problem

rt, you also have to install OpenMPI. -- ---------- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 ---------- Mr. Jussi Lehtola, M. Sc., Do

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 L

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

e distribution. SPEC: https://cvs.fedoraproject.org/viewvc/devel/gromacs/gromacs.spec?view=log -- ---------- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@hels

[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 of

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

as a 7 year support cycle. -- ---------- 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] Gromacs 4 with mpi interface

, you end up starting multiple copies of the simulation instead of a distributed one. -- ------ Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 -------

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

ed I'll put in also 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, Tohtorikoulutett

[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] Gromacs Installation troubles

e gromacs package with $ rpm -ql gromacs -- ---------- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto [EMAIL PROTECTED], p. 191 50623 ---------- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, Universi

Re: [gmx-users] Gromacs Installation troubles

been compiled with. And even if you do compile stuff yourself, it's often easier to take the SRPMs and edit the spec file to make it use the compiler & options you want it to instead of manually compiling & installing the software from the source tar files. -- --

Re: [gmx-users] Gromacs Installation troubles

rce and start from scratch (this is the FreeBSD child > in me talking). Don't use the binary RPMs from gromacs.org, just use Fedora / 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

Re: [gmx-users] Gromacs Installation troubles

g_mdrun (single precision) g_mdrun_d (double precision) 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 Fysiika

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:

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, Tohtori

Re: [gmx-users] Gromacs Installation troubles

he needed dependencies. 3. If you don't want Gromacs 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 -- -------

Re: [gmx-users] FFTW problem for Gromacs4

in the distribution: # 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 PROT

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

sh (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, Tohtorikoulutettav

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

frequency, e.g. you write the output on each step. Also the performance of parallel simulations may be hurt more than of serial simulations, since there is an extra communication step to collect the data. -- -- Jussi

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

SRPMS.newkey/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],

Re: [gmx-users] Fedora port of Gromacs available

On Tue, 2008-10-21 at 10:11 +0300, Jussi Lehtola wrote: > installing GROMACS has just become that much easier. I have made RPMs > that have now been included in Fedora 8 and Fedora 9. The packages are > also available in the Fedora EPEL testing branches > ( http://fedoraproject.o

[gmx-users] Fedora port of Gromacs available

r - tutorial files 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, Tohtori

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

be available at least for RHEL 4, 5 and Fedora 9 and 10. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto [EMAIL PROTECTED], p. 191 50623 -

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 &

[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

[gmx-users] Runtime CPU capabilities detection

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

Re: [gmx-users] Threading in GROMACS

ent distribution has 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 PROTECTE

Re: [gmx-users] Time step in md

able to use larger time steps. With hydrogen bond 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. -- ------ Jus

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

ions running. -- ------ 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 [EMA

[gmx-users] OPLS atom types for THF simulations

working THF OPLS-AA topology I'd very much appreciate it. -- ---------- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto [EMAIL PROTECTED], p. 191 50632 ---------- Mr. Jussi Lehtola,

Re: [gmx-users] Re: Installation gromacs

ANCE MUST YOU 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 Le

Re: [gmx-users] simulations backward in time

ue to rounding errors and a chaotic system. -- ------ Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto [EMAIL PROTECTED], p. 191 50673 ------ Mr. Jussi Lehtola, M. Sc., Doctoral St

Re: [gmx-users] instalation in FC7i386

thout any problems using the default compiler and system 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, Tohtor

Re: [gmx-users] instalation in FC7i386

dora is /usr/bin/cpp . Also Fedora 7 went EOL a couple of weeks ago, so you should consider upgrading to a supported distribution.. -- ------ Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsi

Re: [gmx-users] low cpu usage

s without any problems. Do you have some other processes running on your machines (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

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 see

RE: [gmx-users] Energy minimisation problem

ugh this is a united atom 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 [EM

[gmx-users] Energy minimisation problem

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

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

Anyway, if you 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],

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

nd openmpi-devel, and then use mpicc to compile Gromacs (mpif77 for Fortran 77 and mpif90 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. -- ---

[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

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