Dear Gromacs users,
I have been installing Gromacs on a Power6 4.7 GHz with Infiniband,
GBit-Ethernet
before calling configure, I set:
export LDFLAGS="-L/gpfs/schraven/fftw3/lib"
export CPPFLAGS="-I/gpfs/schraven/fftw3/include"
export CC="mpcc_r -q64"
export CFLAGS="-O3 -qstrict -qarch=auto -qtu
Just a report, and sort of a fix
For parallel md runs of some large systems I get a segmentation fault when
using 8 processors (but not 4).
Using fftw 3.2.2 and openmpi 1.3.3 and gromacs 4.0.5.
I tried different versions of openmpi and fftw, but the only thing that
helped was using mpich2 ins
Ah yes, but can't you configure an automatic server forward to do this? I
can't imagine many people want to manually retype the url they get as a
google result.
On Thu, Jun 4, 2009 at 2:23 PM, Justin A. Lemkul wrote:
>
>
> pim schravendijk wrote:
>
>> Hi,
>>
Hi,
there seems to be a discrepancy between google results from the gromacs
pages and the pages themselves.
If going to results on the mailing list or for example:
www.*gromacs*.org/documentation/howtos/*mpich*_howto.html
I see the gromacs page, and the submenu seems to be ok, but the page is
em
Hi all,
I don't know if this is already known, but I just read that starting
august 1, 2007, the entries in the standard pdb archives will be in
pdb format 3.1.
check the news from july 19 for more details: http://www.wwpdb.org/news.html
Or: http://remediation.wwpdb.org/
The general overview of
Hi People!,
The Gromacs website is seriously broken. I wanted to copy-paste the
line for cvs checkout as I usually do, but following the link to the
CVS page via either the download or the developer menu gives me a page
saying I don't have access and need to log in.
Using the website search func
On 7/31/06, [EMAIL PROTECTED] <[EMAIL PROTECTED]
> wrote:Send gmx-users mailing list submissions toDate: Mon, 31 Jul 2006 07:21:46 -0700
From: "David Mobley" <[EMAIL PROTECTED]>Subject: Re: [gmx-users] langevin dynamicsGerrit is right, with "sd", the friction is set by tau_t, as described
in the se
Also check the even more recent: J. Chem. Theory. Comput. vol 2 (2006) 947
They give a nice introduction on the discussion between T-Stacked and Parallel Displaced benzene-benzene structures.
It appears that the actual conformation of liquid benzene (crystalline
benzene can be a whole different
On 7/20/06,
[EMAIL PROTECTED] <[EMAIL PROTECTED]
> wrote:From: priyanka srivastava <
[EMAIL PROTECTED]>Subject: [gmx-users] atom names do not matchThanks again for your kind response.I guess I will write down my problem once again :-)
Warning: atom names in 96_neatsys14.top and test.grodon't mat
On 7/13/06, [EMAIL PROTECTED] <[EMAIL PROTECTED]
> wrote:From: Susan Chacko <[EMAIL PROTECTED]
>Subject: [gmx-users] Gromacs on Pathscale/Infiniband?Hi all,We have a bunch of Opterons connected with Infiniband. I'm trying toget Gromacs compiled for these nodes. I successfully built FFTW
3.1.2, but
On 7/11/06, [EMAIL PROTECTED]
<[EMAIL PROTECTED]
> wrote:Send gmx-users mailing list submissions to
gmx-users@gromacs.orgFrom: "Berk Hess" <[EMAIL PROTECTED]>Subject: Re: [gmx-users] Energy profile with umbrella sampling
>From: "pim lists" <
[EMAIL PROTECTED]>>>We are using umbrella sampl
On 7/11/06, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote:
Send gmx-users mailing list submissions toMessage: 6
Date: Tue, 11 Jul 2006 17:27:46 +0200From: Steven Kirk <[EMAIL PROTECTED]>
Consider a pair of spherical macromolecules of diameter ~2.5 nm,arranged along an x-axis so that their centres of
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