Hi, there:
I was trying to compile gromacs4.5.1 on a GPU cluster (https://secure.nersc.gov/nusers/systems/dirac/
).
The compilation seems to work fine, but in the installation folder,
only bin/mdrun-gpu presents. Is it supposed to be so?
When I type ./mdrun-gpu -h, the following error
Hi,
if you only want to use the two processors of you laptop you
can simple leave away the --enable-mpi flag. Then it will
work in parallel using threads. Use mdrun -nt 2 -s ...
to specify two threads.
If you anyhow want to compile with MPI, take a look
at the config.log file (search for 'Cannot
Hi all
Is that any one have liquid-liquid interface simulation (like lysozyme by
justin). if so kindly share it through this discussiion forum.it will be of
great help for the newusers like me to use gromacs for liquid-liquid
interface simulation.
Regards
Vinoth
--
gmx-users mailing list
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On 09/27/2010 08:42 PM, simon sham wrote:
Hi,
I wanted to test the GROMACS MPI version in my dual-processors laptop. I
have installed openmpi 1.4.2 version. However, when I tried to configure
GROMACS 4.5.1 with --enable-mpi option, I got the
On 2010-09-28 09.58, vinothkumar mohanakrishnan wrote:
Hi all
Is that any one have liquid-liquid interface simulation (like lysozyme
by justin). if so kindly share it through this discussiion forum.it
http://forum.it will be of great help for the newusers like me to use
gromacs for
Hi,
You don't need MPI within one machine.
Gromacs 4.5 has a built in thread-mpi library that gets built automatically.
Berk
Date: Tue, 28 Sep 2010 10:22:30 +0200
From: domm...@icp.uni-stuttgart.de
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] MPI and dual-core laptop
-BEGIN
Dear fellow Gromacs users
Does anyone know how the -surf mol option works?
I am trying to calculate the coordination number for a molecule in a slice
(xy-plane, delta-z ~ 0.5 nm) of my system. I believe I understand how to do the
integration of the RDF function if I use the center-of-mass
Hi all
I want to run a simulation of one tert-pentane molecule inside one
organic cage molecule. I have the topology files for both molecules but
obviously I only need one .top file as the input for grompp. What is the
most convenient way of having both topologies in one file?
Many Thanks
Gavin
Hi,
g_rdf -surf mol counts the number of atoms within a distance r from the surface,
i.e. the atoms which have a distance of less than r to the closest atom of the
molecule.
Since the surface can be complex and dynamic, normalization is difficult.
Berk
From: ch...@nus.edu.sg
To:
Look up the include file mechanism on the webpage.
Mark
- Original Message -
From: Gavin Melaugh gmelaug...@qub.ac.uk
Date: Tuesday, September 28, 2010 19:04
Subject: [gmx-users] topology file for two molecules
To: Discussion list for GROMACS users gmx-users@gromacs.org
Hi all
I
Hi Mark.
I have looked this up, but I am a little uncertain. Does one of the
topologies have to be included within the other as an .itp file. If so
do I only define the [defaults directive] in the .top file i.e. I take
it I don't include this directive in the .itp file as well.
Cheers
Gavin
Is there any tutorial for liquid-liquid interface in any of the website?.
Regards
Vinoth
On Tue, Sep 28, 2010 at 2:01 PM, David van der Spoel
sp...@xray.bmc.uu.sewrote:
On 2010-09-28 09.58, vinothkumar mohanakrishnan wrote:
Hi all
Is that any one have liquid-liquid interface simulation
vinothkumar mohanakrishnan wrote:
Is there any tutorial for liquid-liquid interface in any of the website?.
If you can't find it at http://www.gromacs.org/Documentation/Tutorials or with
Google, then it probably doesn't exist.
-Justin
Regards
Vinoth
On Tue, Sep 28, 2010 at 2:01 PM,
Gavin Melaugh wrote:
Hi Mark.
I have looked this up, but I am a little uncertain. Does one of the
topologies have to be included within the other as an .itp file. If so
No. You #include .itp files to simply add molecules within a .top; it would be
very rare to #include an .itp within an
Hi Justin
Cheers. I have attached my pentane itp file. The cage itp is formatted
the same. In the examples there never seems to be [atom types] included.
I have included it. Does it seem O.K?
Gavin
Justin A. Lemkul wrote:
Gavin Melaugh wrote:
Hi Mark.
I have looked this up, but I am a
Gavin Melaugh wrote:
Hi Justin
Cheers. I have attached my pentane itp file. The cage itp is formatted
the same. In the examples there never seems to be [atom types] included.
I have included it. Does it seem O.K?
You only need to use an [atomtypes] directive if you're introducing new atom
why don't someone can post the tutorial in the gromacs website? because
gromacs was heavily used for liquid-liquid interface simulation.I hope
probably i will do it in the near future.
Regards
Vinoth
On Tue, Sep 28, 2010 at 4:05 PM, Justin A. Lemkul jalem...@vt.edu wrote:
vinothkumar
O.K
Cheers
Gavin
Justin A. Lemkul wrote:
Gavin Melaugh wrote:
Hi Justin
Cheers. I have attached my pentane itp file. The cage itp is formatted
the same. In the examples there never seems to be [atom types] included.
I have included it. Does it seem O.K?
You only need to use an
Thank you Gonçalo and Dallas for your help.
Best Regards
Anthony
2010/9/27 Gonçalo C. Justino goncalo.just...@gmail.com:
Hi Anthony,
You can use the '-conc' tag from genion during file preparation, as
per http://manual.gromacs.org/current/online/genion.html.
Gonçalo
On 27 September 2010
Dear Gromacs Users and Developers,
I'm currently using Gromacs 4.5 on a Fedora 12 i686 to performed my ionic
liquid MD simulation using amber 99 force field. I got my topology from
topolbuild v 1.3. I successfully minimized both cation and anion separately
using cg and steep. Then I include the
Hi Justin
I Did the following and it worked. You were right about using one atom
types directive. If you don't mind I have another query. In all my
topology files to date (one molecule type), I have always listed the
atomtypes in the [atomtypes] directive, and used the set up in
[defaults] below.
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Hello,
I am really curious that amber has support for Room Temperature Ionic
liquids ? Can you please provide me a reference how this force field
works for this kind of liquids.
/Flo
On 09/28/2010 03:01 PM, Alep Latep wrote:
Dear Gromacs Users
vinothkumar mohanakrishnan wrote:
why don't someone can post the tutorial in the gromacs website? because
The implication from my previous message was that, if you cannot find a tutorial
in an obvious place, one does not exist. There is not a tutorial for every task
that a user may wish
Gavin Melaugh wrote:
Hi Justin
I Did the following and it worked. You were right about using one atom
types directive. If you don't mind I have another query. In all my
topology files to date (one molecule type), I have always listed the
atomtypes in the [atomtypes] directive, and used the
Justin
Cheers, I had just posted a more general query prior to you getting
back? It is perhaps not as vague.
Gavin
Justin A. Lemkul wrote:
Gavin Melaugh wrote:
Hi Justin
I Did the following and it worked. You were right about using one atom
types directive. If you don't mind I have
Roland Schulz wrote:
On Mon, Sep 27, 2010 at 9:58 PM, Mark Abraham mark.abra...@anu.edu.au
mailto:mark.abra...@anu.edu.au wrote:
- Original Message -
From: Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu
Date: Tuesday, September 28, 2010 11:39
Subject:
Hi,
yes that is a bug with cmake (see
http://bugzilla.gromacs.org/show_bug.cgi?id=549).
You can either disable BUILD_SHARED_LIBS and or you can ran make install
as a workaround until the bug is fixed.
Roland
On Tue, Sep 28, 2010 at 3:02 AM, BIN ZHANG zhn...@gmail.com wrote:
Hi, there:
I was
Roland Schulz wrote:
Please make sure that the error exists in the latest version. Either
4.5.1 or if you know how please check the latest GIT version
from release-4-5-patches. If you still get the error with the latest
version, please file a bugzilla report and attach all required files.
Dear gromacs users,
I was planning to study the interaction of a peptide with a zinc
oxide ( ZnO) surface. So, I was wondering whether there is any forcefield for
metal oxide especially for Zinc Oxide ( ZnO) in literarure that you can suggest
that can be used in combination with
Hi,
I was finally able to get my MPI GROMACS running on my laptop. Thanks for all
those who have provided invaluable suggestions.
Best,
Simon Sham
--- On Mon, 9/27/10, simon sham ssha...@yahoo.com wrote:
From: simon sham ssha...@yahoo.com
Subject: MPI and dual-core laptop
To:
--
Found 1048 different hydrogen bonds in trajectory
Found 2292 different atom-pairs within hydrogen bonding distance
Merging hbonds with Acceptor and Donor swapped
2/10915Segmentation fault
__
Hi guys,
I got the msg like above
Yao Yao skrev 2010-09-28 19.25:
--
Found 1048 different hydrogen bonds in trajectory
Found 2292 different atom-pairs within hydrogen bonding distance
Merging hbonds with Acceptor and Donor swapped
2/10915Segmentation fault
Hi Erik,
Sorry about that, I did not notice it.
I used the command line,
g_hbond -f test.trr -s test.tpr -ac test.xvg -e 100 -dt 1
Thanks,
Yao
--- On Tue, 9/28/10, Erik Marklund er...@xray.bmc.uu.se wrote:
From: Erik Marklund er...@xray.bmc.uu.se
Subject: Re: [gmx-users] Fw: g_hbond
Hello i am very new to molecular mechanics so please excuse me if my questions
are a little naive or stupid.I am trying to minimise a mol2 file with
topolbuild1_3 using the following command line arguments from within the
topolbuild directory:
./topolbuild -dir
Hi all,
I am sorry to ask such a question,may it seems very stupid, but I am very
confused about it.
pull_init is the reference distance at t=0. the reference distance is the
distance between the pull group and the reference group? This is a single
value, except for geometry position which
zhongjin wrote:
Hi all, I am sorry to ask such a question,may it seems very stupid, but I am
very confused about it. pull_init is the reference distance at t=0. the
reference distance is the distance between the pull group and the reference
group? This is a single value, except for geometry
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