On Tue, Oct 29, 2013 at 2:21 AM, Neha Gandhi n.gandh...@gmail.com wrote:
Dear Users,
I have a system consisting of peptides and a linear carbohydrate.
Initially I tried to simulate these peptides using virtual sites and
it worked. I can use pdb2gmx for building virtual sites on protein
Hi Justin,
are you guys planning anything to make pdb2gmx understand the CHARMM patch
residues? We have some python scripts which generate new residues based on
the patch residues, which allows us to simulate branched molecules (e.g.
glycosylation or lignin). But that approach is very suboptimal
Hi,
based on Mark's idea I would have thought that the cpu detection would
have already failed during cmake. But it seems it detected SSE4.1
correctly.
Could you post the stack trace for the crash? (see previous mail for
instructions)
Roland
On Sun, Jun 9, 2013 at 4:42 PM, Amil Anderson
Amil,
would it be possible for you to compile with a different compiler?
Ideally gcc 4.7.3. Alternative could you send us the stack for when it
crashes?
For that you need to:
- compile with debug -DCMAKE_BUILD_TYPE=Debug
- run under gdb gdb --arg /path/to/mdrun {your mdrun arguments}
- enter bt
. Amil, please post the cmake output and the
CMakeFiles/CMakeError.log. Because the CPU detection probably also
already failed there if this is the case.
Roland
Mark
On Fri, Jun 7, 2013 at 7:23 PM, Roland Schulz rol...@utk.edu wrote:
Amil,
would it be possible for you to compile
Hi,
I recommend to run the regressiontests. The simplest way is to build
GROMACS with cmake -DREGRESSIONTEST_DOWNLOAD, and run make check.
See
http://www.gromacs.org/Documentation/Installation_Instructions#.c2.a7_4.12._Testing_GROMACS_for_correctness
for more details.
Roland
On Thu, Jun 6,
On Mon, May 20, 2013 at 1:23 PM, Humayun Arafat hasa...@gmail.com wrote:
I am only interested in GPU code.
Is there anyway I can just run this using cray compilers?
Why do you want to use the cray compilers? As Mark said those aren't
supported. We reported the problems with them to Cray but
.
Currently I get error for the atomic.h inside thread_mpi. I think it needs
intrinsics.
Maybe there are some others as well.
Please let me know the issues.
thanks
On Mon, May 20, 2013 at 5:09 PM, Roland Schulz rol...@utk.edu wrote:
On Mon, May 20, 2013 at 1:23 PM, Humayun Arafat hasa
Hi,
you can use catdcd: www.ks.uiuc.edu/Development/MDTools/catdcd/
Roland
On Wed, May 15, 2013 at 3:14 AM, James Starlight jmsstarli...@gmail.com wrote:
Dear Gromacs users!
I want to find possible way for the conversion of the set of the Gromacs's
xtc trajectories to the DCD format.
The
On Tue, Apr 2, 2013 at 5:40 AM, Mark Abraham mark.j.abra...@gmail.comwrote:
IIRC, the default Cygwin gcc is too old to compile GROMACS, as discussed on
this list in the last few months some time. I don't know how easy it is to
get a new one via the Cygwin package system.
Cygwin has the gcc
Hi Raid,
I just tested Gromacs 4.6.1 compiled with ICC 13 and GCC 4.1.2 on CentOS
5.6 and I don't have any problems with pinning. So it might be useful to
open a bug and provide more details, because it should work for CentOS 5.x.
Yes, for pure water the group kernels are faster than Verlet.
On Tue, Feb 5, 2013 at 8:52 AM, Christian H. hypo...@googlemail.com wrote:
Head of .log:
Gromacs version:VERSION 5.0-dev-20121213-e1fcb0a-dirty
Is it on purpose that you use version 5.0 and not 4.6? Unless you plan
development I suggest to use 4.6 (git checkout release-4-6)
I can
On Wed, Feb 6, 2013 at 2:35 PM, Roland Schulz rol...@utk.edu wrote:
On Tue, Feb 5, 2013 at 8:52 AM, Christian H. hypo...@googlemail.comwrote:
Head of .log:
Gromacs version:VERSION 5.0-dev-20121213-e1fcb0a-dirty
Is it on purpose that you use version 5.0 and not 4.6? Unless you plan
On Wed, Feb 6, 2013 at 6:05 PM, jeela keel jeel...@gmail.com wrote:
cmake .. -DGMX_BUILD_OWN_FFTW=ON
Because you already build fftw yourself you don't need GMX_BUILD_OWN_FFTW.
The option means that gromacs builds fftw for you. Instead simply specify
where you installed fftw with
On Tue, Feb 5, 2013 at 8:58 AM, Berk Hess g...@hotmail.com wrote:
One last thing:
Maybe a macro is not set, but we can actually query the number of
processors.
Could you replace the conditional that gets triggered on my machine:
#if defined(_SC_NPROCESSORS_ONLN)
to
#if 1
So we can check
Hi,
make sure to run
source /opt/intel/bin/iccvars.sh intel64
before compiling.
Roland
On Fri, Feb 1, 2013 at 9:06 AM, Fernando Favela ffav...@fis.cinvestav.mxwrote:
Hi justin,
this is the other error message:
[ 56%] Building C object src/mdlib/CMakeFiles/md.dir/genborn_allvsall.c.o
[
On Thu, Jan 31, 2013 at 8:18 PM, Fernando Favela
ffav...@fis.cinvestav.mxwrote:
Dear Gromacs users,
I'm trying to install GMX 4.6 in a 64 Bit Machine with Nvidia GTX 680
cards, I've already installed the intel compilers, cuda 5 and openmpi.
I do the following procedure:
On Tue, Jan 29, 2013 at 11:07 AM, Susan Chacko sus...@helix.nih.gov wrote:
Thanks for the info! Our cluster is somewhat heterogenous, with
some 32-core GigE-connected nodes, some older 8-core Infiniband-connected
nodes, and some GPU nodes. So we need pretty much every variation
of mdrun :-).
On Mon, Jan 21, 2013 at 3:55 AM, Changwon Yang sht_yc...@hotmail.comwrote:
Im trying to run an md or em using an implicit solvation method using
gromacs 4.6 but I always get the incorrect result.
ICC version : icc 11.0
fftw version : 3.2.2
benchmark system is gromacs-gpubench
Hi,
could you check if you get these warnings also with the latest version from
git? We have changed quite a bit sense then.
git clone https://gerrit.gromacs.org/p/gromacs
git checkout release-4-6
Roland
On Tue, Jan 15, 2013 at 9:34 AM, Richard Broadbent
richard.broadben...@imperial.ac.uk
Hi,
thanks for the bug report. Please let us know whether:
https://gerrit.gromacs.org/#/c/2014/
fixes it.
Roland
On Thu, Jan 10, 2013 at 4:08 AM, Albert mailmd2...@gmail.com wrote:
hello:
I am trying to use g_select to make an index file with command:
g_select_mpi -f md.xtc -s
On Wed, Jan 9, 2013 at 3:17 AM, James Starlight jmsstarli...@gmail.comwrote:
As I understood that gromacs version already has included openMM so
the installation of the external openMM sources is not needed, isnt it
?
No the new build in GPU implementation and openMM are two different
Hi,
it seems you are using OpenMM. The recommended approach is to compile with
GMX_OPENMM=off and GMX_GPU=on.
Roland
On Wed, Jan 9, 2013 at 10:45 AM, sdlonga dlo...@caspur.it wrote:
Hi,
I succesfully built the mdrun-gpu on a MacOS MountainLion having one CUDA
NVIDIA GeForce GTX 660
Hi,
is this an implicit water calculation? If so it shouldn't use PME.
Roland
On Wed, Jan 9, 2013 at 2:27 PM, James Starlight jmsstarli...@gmail.comwrote:
Dear Szilárd, thanks for help again!
2013/1/9 Szilárd Páll szilard.p...@cbr.su.se:
There could be, but I/we can't well without
Hi,
g_sans is already in the master version of Gromacs (Justin's link is to
g_nse) but it won't be part of 4.6 instead it will be part of 5.0. You can
get this version from git (git clone git://git.gromacs.org/gromacs.git). As
an alternative you could use http://www.sassena.org/ (disclaimer the
On Sun, Dec 9, 2012 at 11:30 AM, Albert mailmd2...@gmail.com wrote:
Hello:
I am compiling Gromacs4.6beta2 with intel cimpiler by command:
cmake .. -DGMX_MPI=ON
-DCMAKE_CXX_COMPILER=/soft/intel64/icc/bin/intel64/mpiCC
-DCMAKE_C_COMPILER=/soft/intel64/icc/bin/intel64/icc
You shouldn't
Hi,
On Thu, Dec 6, 2012 at 4:58 AM, hubert santuz hubert.san...@gmail.comwrote:
The building/compilation of gromacs itself is working.
But, when I try to compile the template file to create my own plugin, it
fails.
Yes. I broke that for beta1. If you don't want to wait for beta2 or 3 (not
On Thu, Dec 6, 2012 at 9:42 PM, Yorquant Wang wangy...@gmail.com wrote:
Hi Mark:
There is a new instruction set architecture (*Advanced Vector
Extensions
* (AVX)) that can make float calculation in Intel CPU faster two times
compared with the old instruction set. I want to know if the
On Wed, Dec 5, 2012 at 4:14 AM, sebastian
sebastian.wa...@physik.uni-freiburg.de wrote:
The test of the nbnxn_pme setup breaks as well after 50 steps (I
extended the run using tpbconv) with the same lincs warning. (log attached)
AFAIK, attachment aren't supported by the mailing list. Could
On Tue, Dec 4, 2012 at 11:30 AM, sebastian
sebastian.wa...@physik.uni-freiburg.de wrote:
On 12/04/2012 05:09 PM, Mark Abraham wrote:
2fs is normally considered too large a time step for stable integration
with only bonds to hydrogen constrained, so your observation of
non-reproducible
Hi,
a small addition to Mark's answer. If you want/need to use an older gcc
version 4.4.6 and 4.5.3 have the necessary fix too. Also you can disable
AVX with cmake -DGMX_CPU_ACCELERATION=SSE4.1 . But you will get somewhat
lower performance (AFAIK only 10% with group kernels but more with verlet
On Fri, Nov 30, 2012 at 5:01 AM, Carlo Camilloni
carlo.camill...@gmail.comwrote:
Dear All,
I have successfully compiled the beta1 of gromacs 4.6 on my macbook pro
with mountain lion.
I used the latest cuda and the clang/clang++ compilers in order to have
access to the AVX instructions.
Hi,
On Fri, Nov 30, 2012 at 5:01 AM, Carlo Camilloni
carlo.camill...@gmail.comwrote:
1. the compilation was easy but not straightforward:
cmake ../ -DGMX_GPU=ON
-DCMAKE_INSTALL_PREFIX=/Users/carlo/Codes/gromacs-4.6/build-gpu
-DCMAKE_CXX_COMPILER=/usr/bin/clang++
link.txt
file,
while everything works fine by checking out the revision you suggested.
Best,
Carlo
Message: 3
Date: Fri, 30 Nov 2012 08:34:24 -0500
From: Roland Schulz rol...@utk.edu
Subject: Re: [gmx-users] Build on OSX with 4.6beta1
To: Discussion list for GROMACS users gmx-users
On Thu, Nov 29, 2012 at 9:20 PM, Justin Lemkul jalem...@vt.edu wrote:
Hooray for being the first to report a problem with the beta :)
We have a cluster at our university that provides us with access to some
CPU-only nodes and some CPU-GPU nodes. I'm having problems with getting
4.6beta1 to
Hi Raf,
which version of Gromacs did you use? If you used branch nbnxn_hybrid_acc
please use branch release-4-6 instead and see whether that fixes your
issue. If not please open a bug and upload your log file and your tpr.
Roland
On Thu, Nov 15, 2012 at 5:13 PM, Raf Ponsaerts
Hi,
you can use the tpr files from the tgz if you use the non-implicit solv
(preferable PME) test.
Roland
On Wed, Oct 31, 2012 at 10:37 AM, Susan Chacko sus...@helix.nih.gov wrote:
Hi all,
I wanted to test the built-in support in Gromacs 4.6 (non-OpenMM) for GPUs.
I downloaded the latest
Hi,
the OpenMM code is still under review. You can download it using
git fetch https://gerrit.gromacs.org/gromacs refs/changes/83/1283/14 git
checkout FETCH_HEAD
You can check https://gerrit.gromacs.org/#/c/1283/ for the latest version
of it (as of time of writing the above line gives you the
On Fri, Aug 24, 2012 at 12:23 PM, Albert mailmd2...@gmail.com wrote:
Dear:
I use g_tune_pme for MD production but it clashed before the job
finished since it is over cluster walltime limitation. I get the
following information from perf.out:
mpirun -np 144 mdrun -npme -1 -s tuned.tpr -v
Hi,
yes they will all be supported.
For the 650M (GDDR5 model) I get: 58.5 ns/day and only using the CPU
(i7-3610QM) I get: 44.4 ns/day
for 21k atoms water system (rcoulomb .8, spacing: .096, nstlist=7,
CUDA 5, development GPU driver).
So if you are planning to get a similar fast CPU you
On Fri, Jun 8, 2012 at 12:21 PM, Wang, Yuhang ywang...@illinois.edu wrote:
Dear Gromacs developers,
I have benchmarked the desolvation free energy calculation of Na+ ion
using Gromacs and NAMD (for comparison). There is a large difference in the
electrostatic desolvation free energy (see
Hi,
it is always possible that your simulation is isn't well equilibrated and
different rouding errors make it crash with one binary/hardware but not
with another. See also
http://www.gromacs.org/Documentation/Terminology/Blowing_Up. You should
first make sure that this isn't the case by taking a
Hi,
On Sat, May 26, 2012 at 12:42 PM, a a pat...@hotmail.com wrote:
/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/xyzplugin.so: wrong ELF
class: ELFCLASS64
This error suggests that you installed vmd in 64bit but installed Gromacs
in 32bit. Reinstall either to make it match and it should
On Wed, Apr 25, 2012 at 9:38 AM, Szilárd Páll szilard.p...@cbr.su.sewrote:
On Wed, Apr 25, 2012 at 11:43 AM, SebastianWaltz
sebastian.wa...@physik.uni-freiburg.de wrote:
Dear all,
will the new version 4.6 work together with CUDA 4.2? Would be good to
know, since this is needed for the
On Fri, Apr 6, 2012 at 12:24 AM, Peter C. Lai p...@uab.edu wrote:
Sounds like there is a lanugage barrier?
Anyway, some cluster filesystems don't support append (e.g. lustre).
I often use append on lustre. No problem. Why do you think it doesn't work?
So I never use append.
I will use
Hi,
please make sure you compile with support for vmd plugins. One way to check
is that the src/config.h in your build folder contains #define
GMX_DLOPEN. If it does not please check for warnings/errors in the
cmake/configure output and let us know how you run cmake/configure.
If have compiled
Hi,
it is planned for 5.0. Currently you need to manually run it in parallel.
E.g. by split the trajectory into pieces and running the analysis of each
piece in parallel.
Roland
On Sun, Jan 8, 2012 at 1:14 AM, Juliette N. joojoojo...@gmail.com wrote:
Hello all,
I am just wondering if
Hi,
this is on purpose. Since 4.5 GROMACS requires SSE2. It is used for e.g.
the GB kernels. Because CPUs with SSE1 support but no SSE2 are so old we
don't try to support them anymore even for those kernels not requiring SSE2.
Roland
On Tue, Dec 20, 2011 at 6:05 AM, Daniel Adriano Silva M
On Wed, Nov 16, 2011 at 4:11 PM, xianqiang xianqiang...@126.com wrote:
Hi, all
I just restart a simulation with 'mpirun -np 8 mdrun -pd yes -s md_0_1.tpr
-cpi state.cpt -append'
However, the following error appears:
Output file appending has been requested,
but some output files
On Wed, Nov 16, 2011 at 7:57 PM, bharat gupta bharat.85.m...@gmail.comwrote:
Hi,
I was running a simulation of 10ns which crashed in between at 1.7 ns
due to power failure. I used the following command to restart the
simulation form that point:
mdrun -s topol.tpr -cpi state.cpt -append
Hi,
On Mon, Nov 14, 2011 at 2:15 AM, lina lina.lastn...@gmail.com wrote:
On Mon, Nov 14, 2011 at 7:47 AM, Roland Schulz rol...@utk.edu wrote:
Hi,
what file system is this? What operating system on the compute node? In
case
it is a network file system what file system is used underneath
Hi,
what file system is this? What operating system on the compute node? In
case it is a network file system what file system is used underneath and
what operating system is the file server using? What version of GROMACS are
you using?
As you workaround you should be able to run with mdrun
cygwin program and cannot be fixed by
GROMACS. If you want decent IO performance you need to either use Visual
C++ or Msys/MingW (see http://redmine.gromacs.org/issues/448).
Roland
--
*From:* Roland Schulz rol...@utk.edu
*To:* Discussion list for GROMACS users
Hi,
this is currently not possible. Currently you can only do temperature or
Hamiltonian RepEx. As far as I know 4.6 will support both simultaneous. In
the mean time you might be able to accomplish your goal
by reformulating the Temp-RepEx as a Hamiltonian RepEx as is done in the
newer version of
Hi,
for Hamiltonian RepEx you need to formulate the different states as a
function of lambda. Look at the free energy documentation to see how to
describe different tables for different lambdas.
Roland
2011/11/8 杜波 2008d...@gmail.com
dear teacher,
if i want to do remd with different
On Tue, Nov 8, 2011 at 5:59 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 8/11/2011 11:35 PM, Szilárd Páll wrote:
Additionally, AFAIK you will get better performance if you compile
with MSVC which should be fairly easy if you use CMake - I'm not
entirely sure about this
I'd be
On Wed, Sep 21, 2011 at 9:01 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 21/09/2011 7:27 PM, zhongjin wrote:
Dear GMX users:
While I am installing gmx4.5.5, an error occured after make command :
cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2
Hi,
you can use trjconv for that (or editconf). You probably would want to add
some waters though.
Roland
On Thu, Aug 18, 2011 at 2:50 PM, Peter C. Lai p...@uab.edu wrote:
Is there anyway I can extract a subset of atoms from a cpt file, like I can
with trjconv operating on a traj file? I
On Thu, Aug 18, 2011 at 3:02 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Roland Schulz wrote:
Hi,
you can use trjconv for that (or editconf). You probably would want to
add some waters though.
For trjconv, you can get a coordinate file, but not a .cpt; editconf throws
a
fatal
/release-4-5-patches
fatal: git checkout: updating paths is incompatible with switching
branches.
Did you intend to checkout 'origin/release-4-5-patches' which can not be
resolved as commit?
Is this a problem of the server I am using or is it just a misuse of git?
Thanks
2011/3/22 Roland
On Sat, Jun 18, 2011 at 4:13 PM, chris.ne...@utoronto.ca
chris.ne...@utoronto.ca wrote:
Dear Users:
If I create the topology of a peptide like this:
pdb2gmx -f protein.gro -vsite hydrogens
And then simulate it in vacuum, is lincs used at all? I believe that
it is, as if I use a timestep
My understanding is that the v-site algorithm is used for the virtual sites
and LINCS is used for bonds not involving v-sites (and also angles if you
choose contraint=angles).
On Sat, Jun 18, 2011 at 4:40 PM, chris.ne...@utoronto.ca
chris.ne...@utoronto.ca wrote:
Thank you Roland.
I did use:
this is fixable?
Thanks,
Dimitar
On Sun, Jun 5, 2011 at 6:20 PM, Roland Schulz rol...@utk.edu wrote:
Two comments about the discussion:
1) I agree that buffered output (Kernel buffers - not application
buffers) should not affect I/O. If it does it should be filed as bug to the
OS. Maybe
Two comments about the discussion:
1) I agree that buffered output (Kernel buffers - not application buffers)
should not affect I/O. If it does it should be filed as bug to the OS. Maybe
someone can write a short test application which tries to reproduce this
idea. Thus writing to a file from one
On Mon, May 9, 2011 at 6:28 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 10/05/2011 12:50 AM, maria goranovic wrote:
Dear experts
I have a protein simulation in a water box. I now want to write a
trajectory containing only the protein, and water molecules within 5
Angstroms of the
Hi,
there is no tool to do that. Trajectories assume to have the same number of
atoms per frame. What you can do is use g_order (it gives you the water
sorted by distance and the number of water within .5nm) or g_select (it can
give you an index file with the atoms within .5nm for each frame)
On Thu, Apr 28, 2011 at 10:05 AM, Bruno Monnet bruno.mon...@hp.com wrote:
Hi,
I'm not really a Gromacs user, but I'm currently benchmarking Gromacs 4.5.4
on a large cluster. It seems that my communication (PME) is really high and
gromacs keeps complaining for more PME nodes :
Average
This seems to be a problem with your MPI library. Test to see whether other
MPI programs don't have the same problem. If it is not GROMACS specific
please ask on the mailinglist of your MPI library. If it only happens with
GROMACS be more specific about what your setup is (what MPI library, what
Hi,
load imbalance is only a performance issue.
Load balancing affects binary reproducibility (meaning the exact same value)
but not accuracy (those it can differ but only within the same accuracy).
Binary reproducibility should only be important for testing purposes, thus
you should use load
Forwarding this email from my group colleague:
Dear Gromacs users,
I am trying to simulate a cellulose fiber in an ionic liquid solution in the
NPT ensemble. During the simulation, the entire system is coupled to a
thermostat. Yet, I observe an inhomogeneous temperature distribution
Hi,
depends on the tool. If the tool just need the coordinates or just
velocities (dcd/vel) you don't need to convert anything because the tools
can use the VMD plugins to read dcd. If the tool needs a tpr file (e.g.
carges) than you need to create one. In most cases the easiest solution to
do
Hi,
this question has been answered often. Please check the archive before
posting.
Roland
On Thu, Mar 31, 2011 at 8:01 PM, parichita parichita
parichitamajum...@yahoo.co.in wrote:
Hi...
I am try to istalling gromacs -4.5.3 on AMD phenom II.
I am following the installtions protocols, 1 St
On Tue, Mar 22, 2011 at 10:26 AM, Ye MEI y...@itcs.ecnu.edu.cn wrote:
Thank you for the new version of gromacs.
But the compilation of gromacs failed on my computer. The commands are as
follows:
make distclean
export CC=icc
export F77=ifort
export CXX=icc
export CFLAGS=-xS
Hi,
try to move your files into your cygwin home directory before
compiling. If that doesn't work, try to first compile a hello world C
program to see why the compiler doesn't work.
Roland
On Tue, Mar 22, 2011 at 12:13 PM, vijaya subramanian
vijay...@hotmail.com wrote:
Hi
I am trying to
On Mon, Mar 21, 2011 at 9:09 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Nancy wrote:
Hi All,
I've used used Gromacs under Linux, and I'm wondering whether it can be
used under Windows 7 and/or Snow Leopard (10.6.6).
Theoretically, Gromacs is compatible with any environment provided you
you can clone from http://repo.or.cz/r/gromacs.git if you have problems with
a proxy.
On Mon, Mar 21, 2011 at 10:54 PM, Alif M Latif prism_d...@yahoo.com wrote:
Dear Gromacs Developers,
Just dropping by to say THANK YOU for v4.5.4, surely is updated version of
4.5.3 with all the bugfixes
Hi,
in most cases the easiest way is to regenerate the topology in
pdb2gmx. If that is not possible for some reason, you can use a
version of psfgen we developed in our lab:
http://www.benlabs.net/psfgen+top/Overview.html
BTW: Please don't cross-post to both gmx-users and gmx-developers.
Roland
Hi,
are you running in parallel (either MPI or threads)? Load-balancing is one
reason for different rounding errors.
You can run with mdrun -reprod to avoid any different rounding between
runs and should in general get the same then.
Roland
On Fri, Jan 28, 2011 at 6:17 PM, Matthew Chan
Yes. But it is better to use the same version. Otherwise you can't set all
parameters (e.g. nstcalcenergy)
Roland
2011/1/26 gromacs ptf1...@163.com
Hi guys,
I created my .tpr through my own desktop (without parallel) using gromacs
4.0.7.
can i run .tpr parallelly using Gromacs
2011/1/10 Camilo Andrés Jimenez Cruz camilo.jimen...@gmail.com
Hi list!
it has been discussed in other posts the inconvenience of PBCing after
rotating (see example:
http://oldwww.gromacs.org/pipermail/gmx-developers/2009-November/003754.html),
I just want to know what is the state of this
Hi,
what is the standard deviation and drift? Are you sure this is a significant
difference to 1?
Roland
On Sun, Dec 26, 2010 at 12:28 AM, sreelakshmi ramesh
sree.laks...@research.iiit.ac.in wrote:
Dear users,
I did nvt equil and after that npt equilbriation and i am
using
You want to compile fftw with either --enable-shared or with --with-pic. Or
you need to compile a static version of Gromacs. As the message says you
can't use fftw without pic with shared libraries in GROMACS.
Roland
On Mon, Dec 20, 2010 at 6:31 PM, Chris Neale chris.ne...@utoronto.cawrote:
experience to the wiki pages. Good documentation
requires many people to help. The (main) developers are often too busy too
write detailed documentation.
Roland
From: Roland Schulz rol...@utk.edu
Subject: Re: [gmx-users] cmake -- relocation R_X86_64_32S against `a
local symbol' can not be used
Chris,
sorry I didn't pay attention (was in a hurry). I know that you have helped
with the documentation and wouldn't have suggested to you to put it on the
wiki if I recognized it was you. I thought it was a new user. And I didn't
want to criticize but only point out (to the assumed new user)
What MVAPICH version are you using?
Are you using a TPR file you know is running fine on some other machine?
Does the 4.5.2 version they installed run correct? If so what is the
configure line they used?
Roland
On Thu, Dec 9, 2010 at 5:14 PM, J. Nathan Scott
scot...@chemistry.montana.edu
What cmake version are you using?
On Wed, Dec 8, 2010 at 9:49 AM, Keith Callenberg kmc...@pitt.edu wrote:
Hello gmx-users,
I am trying to build gromacs-4.5.3 with GPU support with OpenMM. I
have followed the INSTALL-GPU instructions along with the tips given
in this post:
Hi,
you can use trjconv to write frames to GRO format. Or you can use it to
write a trajectory from a different starting point (and then you can use
gmxdump).
Roland
On Wed, Dec 1, 2010 at 4:39 PM, Silvia Crivelli sncrive...@ucdavis.eduwrote:
Hello,
Is there a function that allows users to
On Wed, Dec 1, 2010 at 4:30 PM, Hassan Shallal hshal...@pacific.edu wrote:
Dear Gromacs users,
I am trying to use CHARMM27 taking the simulation conditions of two recent
articles as guides in optimizing the simulation parameters. *(DOI:
*10.1021/ct900549r
and *DOI:* 10.1021/jp101581h).
Baofu,
what operating system are you using? On what file system do you try to store
the log file? The error (should) mean that the file system you use doesn't
support locking of files.
Try to store the log file on some other file system. If you want you can
still store the (large) trajectory
...@gmail.com wrote:
Hi Roland,
Thanks a lot!
OS: Scientific Linux 5.5. But the system to store data is called as
WORKSPACE, different from the regular hardware system. Maybe this is the
reason.
I'll try what you suggest!
regards,
Baofu Qiao
On 11/26/2010 04:07 PM, Roland Schulz wrote
=10,hard,rsize=65536,wsize=65536,timeo=600,addr=172.30.100.219)
On 11/26/2010 05:41 PM, Roland Schulz wrote:
Hi Baofu,
could you provide more information about the file system?
The command mount provides the file system used. If it is a
network-file-system than the operating system and file
On Mon, Nov 22, 2010 at 2:55 PM, Sanku M msank...@yahoo.com wrote:
Hi,
When using gromacs 4.5.3, I experienced two problems ( neither of which
exist in gromacs 4.0.7 or older version like 3.3.3)
1. when issuing grompp command to start one of my simulations, gromacs
4.5.3 gives me fatal
On Sun, Nov 21, 2010 at 2:05 PM, Spitaleri Andrea
spitaleri.and...@hsr.itwrote:
Hi,
yes sure. Basically I do:
1. mdrun -s runA_ -deffnm runA_ -replex 5000 -multi 5 - i get the first
5x25ns of remd simulation (five xtc every 5ps and five trr every 20ps, for
each replica). I check those files
Little bit more background/context would help.
Do you try to compile an all static library? If so you of course need a
static library of fftw. If it is not all static it normally should accept
the dynamic fftw. Then please give us the full configure line, the gcc
command line of the link step and
If you compile using cygwin than it should be able to compile ngmx if you
have all required X11 libraries. I recommend you to use VMD.
On Wed, Nov 10, 2010 at 11:03 PM, bharat gupta bharat.85.m...@gmail.comwrote:
I am trying to run the simulation trajectory using ngmx in windows .. but
it
Hi,
as you output says. It infinite long trajectory. Either set a number of
steps (in mdp file or with tpbconf) or set a maximum time with (mdrun -maxh)
Roland
On Tue, Nov 9, 2010 at 9:03 PM, lin hen cutey...@live.com wrote:
Hi,
I am using the dhfr gpu benchmark with
Could it be that you don't have write permissions in that folder?
Roland
On Tue, Nov 9, 2010 at 12:58 AM, priyam saxena priyam...@gmail.com wrote:
Hey everybody,
Eveytime I use the editconf command, it gives an input/output error in form
of my output.gro file.
This is the command i've
Hi,
the reason turned out to be that the lock daemon (lockd) on the NFS server
was hanging. The error could be found by dmesg.
BTW: Is it somehow possible to print the kernel error messages that are
shown by dmesg to the user from within GROMACS? That would help the user to
directly see the
Hi,
since this is such a simple problem I suggest to simply write a program to
do it. I suggest to start with either the xdrfile library or with the the
template (available under share). My experience is writing those small
things myself is much faster than searching the net and asking on the
Hi,
you could find the number of waters around each using g_order. Then you
would need to have a small script to combine the two lists to find only the
ones close to both.
Roland
On Sat, Oct 23, 2010 at 7:47 AM, leila karami karami.lei...@gmail.comwrote:
Hi gromacs users
Since I study
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