I am trying to do some folding simulations in GROMACS. I saw few mails in the
list stating that implicit water model will be available in GROMACS 4.0
version.
However, I have not found anything on the implicit model in the manual. I am
currently using GROMACS 4.0.7 version. Is it possible to ru
I have some problem about simulating an iron-sulfur bond.
I got the following grompp error message
"No default G96Bond types"
"No default G96Angle types"
"No default G96Proper Gih types"
What should I do to resolve this problem?
Many thanks
Yuranat,
--
gmx-users mailing listgmx-users@gromac
Hi GROMACSers,
I am running into an interesting problem while propagating a long MD
trajectory for a short
peptide. I am using the checkpoint files for restart and tpbconv for
extending the trajectory length, as recommended in the on-line manual
pages. The trajectory is calculated in 10 ps
GMX-USERS,
When I try to scale up from 64 processors to 128 processors my simulation
stops running after a few thousand steps. I'm currently using the abe
supercomputer and in the error file I get the following message:
Warning! Rndv Receiver is receiving (3200 < 4800) less than as expected
Any
Hi
I´m using GROMACS 4.0.7 with the Amber99sb forcefield.
I keep getting an error when I´m typing this command:
pdb2gmx -f t.pdb -o t2.pdb -ff amber99sb -water tip3p
I get this message:
WARNING: atom H is missing in residue SER 2 in the pdb file
You might need to add atom H to the hydr
Dear Moeed:
It seems to me that you are using not the best force field of the
polymer. Why do you apply constaints (LINCS warnings...)? As for the
compression degree and warnings, one cannot say anything sane about
your system without looking at the concrete molecular patterns and
probably dynamic
Dear Dr. Chaban,
Thanks for you answer. Actually, I meant I have a .. system :). If you
remember I was trying to compress my system (PE only) to attain the density
I want. I worked on that problem for nearly one week and I posted the
procedure I used to reach what I want. Unfortunately, no one got
Subject: trjcat : Magic Number Error in XTC file (read 0, should be 1995)
Dear Gromacs Users,
I am trying to cat the .xtc files using the trjcat option in gromacs,
but i am getting an error
Program gmxcheck, VERSION 4.0.7
Source code file: xtcio.c, line: 85
Fatal error:
Magic Number Error in XT
On 23.07.10 10:30, KACHMAR Ali wrote:
> Hi Flor
>
> Thank you very much for your help. I don't know what's wrong in my
> mac. I successfully installed gromacs, and when I restart my mac, I
> tried one of gromacs commands but it did not show up.
>
> It is realy strang, I have to compile again or w
Hi Flor
Thank you very much for your help. I don't know what's wrong in my mac. I
successfully installed gromacs, and when I restart my mac, I tried one of
gromacs commands but it did not show up.
It is realy strang, I have to compile again or what?
Ali
Date: Fri, 23 Jul 2010 10:04:03 +0200
On 23.07.10 09:32, KACHMAR Ali wrote:
> Hi,
>
> I had already installed xcode.
>
> I would like to be sure if it is correct my .bash_profile concerning
> the gcc and mpicc
>
> export PATH=/usr/local/bin:$PATH
If you have a broke installation of gcc and/or mpicc in /usr/local/bin
then the compila
Hi,
I had already installed xcode.
I would like to be sure if it is correct my .bash_profile concerning the gcc
and mpicc
# Setting PATH for Python 2.7# The orginal version is saved in
.bash_profile.pysavePATH="/Library/Frameworks/Python.framework/Versions/2.7/bin:${PATH}"export
PATH
# Setti
Hi,
no just download the Apple Developer Tools from the Apple Developer
page. This will provide the latest version Apple builds of XCode, gcc,
and OpenMPI. Here is the link:
http://developer.apple.com/technologies/tools/
Hope this helps.
Cheers,
Flo
On 22.07.10 20:13, KACHMAR Ali wrote:
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