Hi,
Thanks for your reply. But the problem still persists. Even now I am not able
to download.
-Original Message-
From: gmx-users-boun...@gromacs.org on behalf of Mark Abraham
Sent: Fri 6/7/2013 8:14 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Unable to download
They're still fine. There must be a problem at your end, I'm afraid.
Mark
On Sat, Jun 8, 2013 at 10:46 AM, Bhamy Maithry Shenoy
bhamymait...@aero.iisc.ernet.in wrote:
Hi,
Thanks for your reply. But the problem still persists. Even now I am not
able to download.
-Original
Seems something http://www.gromacs.org/Documentation/Terminology/Blowing_Up,
probably because there is something nonsensical about your starting
configuration. Try to simplify things, visualize the configuration, don't
ignore warnings.
Mark
On Sat, Jun 8, 2013 at 7:10 AM, maggin
Hi Tsjerk,
[I am reposting it since my previous attachment was unable to proceed I
guess]
Thank you for the reply. I am sorry but I don't have the snapshots with me
as my system was formatted and I lost that information. However, I
performed PCA again on Calpha atoms and this time my matrix is
I too cannot download (tried with 3.3 4.5.5 4.6 and 4.5.7).
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Sat, Jun 8, 2013 at 4:05 PM, Mark Abraham mark.j.abra...@gmail.comwrote:
They're still fine. There must be a problem at your end, I'm afraid.
Mark
On Sat, Jun 8, 2013 at
I just downloaded the 4.5.7 tarball to a machine in Australia.
Mark
On Sat, Jun 8, 2013 at 1:23 PM, Chandan Choudhury iitd...@gmail.com wrote:
I too cannot download (tried with 3.3 4.5.5 4.6 and 4.5.7).
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Sat, Jun 8, 2013 at 4:05
As a work-around, you can try to get archives from
https://github.com/gromacs/gromacs/tags (but these will not quite match the
official tarballs - but in ways that don't matter for simulating).
Mark
On Sat, Jun 8, 2013 at 1:54 PM, Mark Abraham mark.j.abra...@gmail.comwrote:
I just downloaded
On 08.06.2013 10:46, Bhamy Maithry Shenoy wrote:
Hi,
Thanks for your reply. But the problem still persists. Even now I am not able
to download.
Can you download from this link?
ftp://ftp.gromacs.org/pub/gromacs/
--
gmx-users mailing listgmx-users@gromacs.org
Thanks a lot. I could download from this link. Is is the latest version?
-Original Message-
From: gmx-users-boun...@gromacs.org on behalf of Mark Abraham
Sent: Sat 6/8/2013 5:27 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Unable to download Gromacs source tar file
I could not download from the mentioned link.
-Original Message-
From: gmx-users-boun...@gromacs.org on behalf of Mirco Wahab
Sent: Sat 6/8/2013 5:42 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Unable to download Gromacs source tar file
On 08.06.2013 10:46, Bhamy
Hello:
I generate a ligand toplogy by ACPYPE with amber GAFF. However, I
found that in the ligandGMX.itp file, in the atomtypes section, the mass
and charge are all zero, like:
[ atomtypes ]
;name bond_type mass charge ptype sigma epsilon Amb
NT NT
On 2013-06-08 17:28, Albert wrote:
Hello:
I generate a ligand toplogy by ACPYPE with amber GAFF. However, I
found that in the ligandGMX.itp file, in the atomtypes section, the mass
and charge are all zero, like:
[ atomtypes ]
;name bond_type mass charge ptype sigma epsilon
Date: Sat, 8 Jun 2013 13:57:51 +0200
From: Mark Abraham mark.j.abra...@gmail.com
Subject: Re: [gmx-users] Unable to download Gromacs source tar file
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID:
On 08.06.2013 14:39, Bhamy Maithry Shenoy wrote:
Can you download from this link?
ftp://ftp.gromacs.org/pub/gromacs/
I could not download from the mentioned link.
Then, your provider/router and/or your network
configuration is blocking FTP port traffic (Port 21),
but not HTTP port traffic
On 06/08/2013 06:56 PM, David van der Spoel wrote:
the ones in the atoms section are the ones that are used UNLESS they
are not given, in which case the defaults are used.
IC.
thank you very much.
Albert
--
gmx-users mailing listgmx-users@gromacs.org
Hello:
Recently I found a strange question about Gromacs-4.6.2 on GPU
workstaion. In my GTX690 machine, when I run md production I found that
the ECC is on. However, in my another GTX590 machine, I found the ECC
was off:
4 GPUs detected:
#0: NVIDIA GeForce GTX 590, compute cap.: 2.0,
Hi Ankita,
It is important to use the correct names for things. The projection is the
(scalar) inner product of the configuration (coordinates) with the
eigenvector. This is also named the score of the configuration on the
selected eigenvector. With g_anaeig -proj you get the projection. Each
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