Hi sh-karbalaee,
Well, running an MD simulation has nothing to do with genion per se.
But it's better not to have a net chare in your system. Therefore
you'd best add an ion (at the least) to your system with unit charge.
Whether you do that using genion or do it by hand, is entirely up to
you.
Dear All,
I am running a simulation for a RNA system using 50 cpus with gromacs
3.3.1. At some frames, my molecule is broken, that is parts of the molecule are on
opposite sides of the periodic box. This problem was reported sometime ago
(Nov. 2006) and David suggested to submit the
This is probably a visualization artifact, since mdrun does not make a
break bonds to generate fragmented molecules.
-Justin
Nguyen Hoang Phuong wrote:
Dear All,
I am running a simulation for a RNA system using 50 cpus with gromacs
3.3.1. At some frames, my molecule is broken, that is
Dear Berk (and whoever else might provide assistance)
I have included also my topology file topol.tpr at
http://drop.io/gmxpull/topol.tpr.
From this you can clearly see that there is no pressure coupling in my
pulled system.
I still have not resolved the issue of the fluctuation artefacts.
Hi List,
We currently have access to a IBM p595 located elsewhere from our lab.
I am trying to install Gromacs on it through ssh.
I could not install FFTW 3.1.2 but managed to install FFTW 2.1.5.
After installing fftw, I followed the installation guidelines
(CPPFLAGS etc) and tried to install
Senthil Kumar M wrote:
However, I have included the one
instance of error as given below:
./configure --prefix=$HOME/gro333 --disable-largefile --with-fft=fftw2
--disable-fortran
followed by
make gives:
xlc_r: 1501-224 fatal error in /usr/vac/exe/ipa64: signal 24 received
make: 1254-004 The
Many thanks in advance,but the problem seems to be solved just by not
including the new residue name in the aminoacids.dat file, despite the
instruction to do so in sec.5.5.1 chapter 5 Topologies of the manual.
Can you tell me if this procedure is correct?
Thanks again
Carmen
Hi Carmen,
You
Hi Carmen,
Well, adding a residue to aminoacids.dat only makes sense for amino
acids (although I admit to fiddle it sometimes, in which case it is
usually best to make a local copy). But one thing with amino acids is
that backbone -N(H)-Ca-C(O)- thing, which is referred to in the
termini
I'm new to gromacs and the past week or so I've been digging through the
archives so that I can simulate a carbon nanotube. I've been able find
coordinates for the carbon nanotube as well as the parameters for the
force field. My question is:
Do I define the parameters in the force field file or
I would recommend reading lots of tutorial material and the Gromacs
manual, especially Chapter 5. There are also numerous posts from Chris
Stiles that contain a link to a tutorial he set up a while back for
doing CNT simulations.
The main point is that you need to generate a topology that
On Thu, Jun 19, 2008 at 12:48 PM, Mark Abraham [EMAIL PROTECTED] wrote:
Senthil Kumar M wrote:
make gives:
xlc_r: 1501-224 fatal error in /usr/vac/exe/ipa64: signal 24 received
make: 1254-004 The error code from the last command is 251.
Stop.
make: 1254-004 The error code from the last
Senthil Kumar M wrote:
On Thu, Jun 19, 2008 at 12:48 PM, Mark Abraham [EMAIL PROTECTED] wrote:
Senthil Kumar M wrote:
make gives:
xlc_r: 1501-224 fatal error in /usr/vac/exe/ipa64: signal 24 received
make: 1254-004 The error code from the last command is 251.
Stop.
make: 1254-004 The error
Justin A. Lemkul wrote:
I would recommend reading lots of tutorial material and the Gromacs
manual, especially Chapter 5. There are also numerous posts from Chris
Stiles that contain a link to a tutorial he set up a while back for
doing CNT simulations.
I agree, and note that there's some
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