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
Fysiika
On Mon, 2008-11-17 at 16:59 -0800, Nicholas Geraedts wrote:
> I'm trying to get Gromacs installed on our systems, but I've been
> running into one error after another. We are running CentOS5 x86-64
> with all the latest updates.
>
>
> I've got the following packages downloaded
> lam-7.1.4
> fftw-
I have solved the reported problem by adding --disable-largefile to
the configure options. Now the non-parallel version compiles and
installs fine. What is the file size limit now? Is it 2 GB?
But now I have problem with the parallel (MPI) version. When I issue
the command:
./configure --prefix=/h
Hi. When I was trying to do the test run for my installed gromacs, I got
message below return to me even though i've source GMXRC (source
/usr/local/gromacs/bin/GMXRC). Can some one tell me why? Thanks.
bcsb09s-imac52:bin bcsb09$ ./gmxtest.pl all
102 out of 102 simple tests FAILED
sh: grompp.out:
Hello,
Can someone tell me if Gromacs will run on SuSe linux enterprise edition,
with an AMD opteron processor?
Thanks in advance,
Marudachalam.
--
Marudachalam S
India
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Andrei Neamtu wrote:
Hello,
Where can be found more information on test particle insertion method
as implemented in gromacs? It is possible to use molecules as test
particles?
Have you search the manual? It answers your second question.
Mark
___
gmx
Hello,
Where can be found more information on test particle insertion method
as implemented in gromacs? It is possible to use molecules as test
particles?
Thank you a lot,
Andrei
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Q. Y. HUAN wrote:
Dear gmx users and developers,
Currently I am installing Grace into my computer, but the problem is that I
found difficulty to install it because there is no complete version of
installation file of it. After i installed the missing files, I install Grace
again but when I wa
Dear gmx users and developers,
Currently I am installing Grace into my computer, but the problem is that I
found difficulty to install it because there is no complete version of
installation file of it. After i installed the missing files, I install Grace
again but when I want to run xmgrace in
Nicholas Geraedts wrote:
I'm trying to get Gromacs installed on our systems, but I've been
running into one error after another. We are running CentOS5 x86-64 with
all the latest updates.
I've got the following packages downloaded
lam-7.1.4
fftw-3.2
gsl-1.11
gromacs-4.0
I installed them in th
I'm trying to get Gromacs installed on our systems, but I've been running
into one error after another. We are running CentOS5 x86-64 with all the
latest updates.
I've got the following packages downloaded
lam-7.1.4
fftw-3.2
gsl-1.11
gromacs-4.0
I installed them in the following order with the fo
Arthur Roberts wrote:
Dear Eudes,
You need to technically make it 1 "big molecule". As long as there are
no bonds specified between molecule A and B. The big molecule will
behave as if there are two molecules in it. I do it to dock small
molecules to proteins.
That's a good description,
Dear Eudes,
You need to technically make it 1 "big molecule". As long as there
are no bonds specified between molecule A and B. The big molecule
will behave as if there are two molecules in it. I do it to dock
small molecules to proteins.
Steps running Gromacs 3.3.3:
1) Combine molec
Dear all,
this is the first time I have experienced any problem with Gromacs
compilation! Of course till now I have been using simple desktop PCs
(both 32 bit and 64 bit) with regular Linux OS (Fedora, Ubuntu etc.).
Now I tried to compile gromacs-4.0.2 on a parallel environment of IBM
P690 Regatta
Hello,
when I start the simulation my box vectors are the following :
16.89660 2.61581 2.07800 0.0 0.0 -0.43665 0.0
0.0 0.0
and with the command (the final written step was at 40487):
trjconv -f traj.trr -dump 40487 -o out.gro
I got these box vectors:
22.35607
Hi,
The triclinic skew factor seems extremely small.
What are your box vectors?
Berk
Date: Mon, 17 Nov 2008 18:26:54 +
From: [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Subject: [gmx-users] error: triclinic skew factor - number of DD cells
Hello,
while I 'm executing an md run I came accr
Hello,
while I 'm executing an md run I came accross this error:
Fatal error:
The X-size of the box (22.541477) times the triclinic skew factor (0.317120) is
smaller than the number of DD cells (8) times the smallest allowed cell size
(0.895000)
My system is monoclinic (sub-categorie to triclini
The first circular for FOMMS 2009 is reproduced in this email below.
Please forward to anyone who would be interested.
Fourth International Conference Foundations of Molecular Modeling and
Simulation
FOMMS 2009
Foundations for Innovation
Semiahmoo Resort, Blaine, WA, USA
July 12 -16, 2009
http
Eudes Fileti wrote:
The error you report is potentially of the everyday
http://wiki.gromacs.org/index.php/blowing_up variety. See
http://wiki.gromacs.org/index.php/Errors#1-4_interaction_not_within_cut-off
First, get your separated-molecules topology and initial structure
working for basic MD.
Hi Mark, sorry, but could you be more specific whenyou say "Combine the
topologies"?
Was not it what I had done early?
Thank you
eef
> The error you report is potentially of the everyday
> http://wiki.gromacs.org/index.php/blowing_up variety. See
>
http://wiki.gromacs.org/index.php/Errors#1-4_inte
DimitryASuplatov wrote:
Hello,
I want neutralize negative charge in my structure. I use genion to add
80 Na and 71 Cl. Than I edit top file manually to decrease SOL number by
151 and add two lines for ions. Since I use OPLSAA they should look like
this (considering names in gromacs/share/gromacs/
DimitryASuplatov wrote:
Hello,
I want neutralize negative charge in my structure. I use genion to add
80 Na and 71 Cl. Than I edit top file manually to decrease SOL number by
151 and add two lines for ions. Since I use OPLSAA they should look like
this (considering names in gromacs/share/gromac
[EMAIL PROTECTED] wrote:
Hi,
I use Gromacs for protein folding studies. I was going through the
existing bugs listed for different versions of gromacs in bugzilla, and
found that many have been resolved. My question is where do i find these
bug resolved Gromacs versions?
For example in version
[EMAIL PROTECTED] wrote:
Hi,
I use Gromacs for protein folding studies. I was going through the
existing bugs listed for different versions of gromacs in bugzilla, and
found that many have been resolved. My question is where do i find these
bug resolved Gromacs versions?
For example in version 3
Hello,
I want neutralize negative charge in my structure. I use genion to add
80 Na and 71 Cl. Than I edit top file manually to decrease SOL number by
151 and add two lines for ions. Since I use OPLSAA they should look like
this (considering names in gromacs/share/gromacs/top/ions.itp)
NA+
Hello,
I`ve been using gromacs 4 since the release and have experienced no
problems or artifacts during simulations. When I ran gmxtest-3.3.3
(./gmxtest.pl all) I`ve received the following error message:
= START =
All 16 simple tests PASSED
All 14 complex tests PASSED
All 6
On Nov 16, 2008, at 12:47 PM, Mark Abraham wrote:
Apologies to people receiving this from the FFTW list too, but it
should be of interest to a large slice of people using GROMACS. In
particular, the improvements for SIMD and size of multiples of 5/10
should be of value for lots of people.
Hi,
I use Gromacs for protein folding studies. I was going through the
existing bugs listed for different versions of gromacs in bugzilla, and
found that many have been resolved. My question is where do i find these
bug resolved Gromacs versions?
For example in version 3.3.3, there is a bug listed
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