Hi ALL,
This may sound like a very basic question, but I am still pondering over it.
I have simulated a membrane protein system for 30 ns after Steepest Descent
minimization and now I want to perform NMA. From the help pages what I
understand is that I need a very well minimized system (using l-bf
On 27/04/10 14:35, vani ms wrote:
plz can anybody tl me if i get "step 0 segmentation fault" in md run of
position restrain step, what does it mean and how can it be solved.
We can't help you unless you provide a lot more information. See
http://www.gromacs.org/Support
Mark
--
gmx-users mai
plz can anybody tl me if i get "step 0 segmentation fault" in md run of
position restrain step, what does it mean and how can it be solved. plz help
me
--
WITH REGARDS
VANI
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Mark, thanks. It resolves my problem.
2010/4/21 Mark Abraham
> On 21/04/2010 4:14 PM, shuqi zhao wrote:
>
>> Dear all,
>> I am compiling gromacs 4.0.7 on AIX 5.3 with "./configure --enable-mpi
>> --enable-ppc-sqrt=1 --enable-ppc-altivec --disable-fortran
>> --with-fft=fftw3". The source codes un
Qian Wang wrote:
Hi,
I use Gromacs4.0.5 to run a 20 ns npt simulation in periodic boundary
box. At first I put peptide in the center of the box, then I write
comm_mode = linear in *mdp file. However, the peptide still moves out of
the box and go through to the other side of the box. Is the
Hi,
I use Gromacs4.0.5 to run a 20 ns npt simulation in periodic boundary box. At
first I put peptide in the center of the box, then I write comm_mode = linear
in *mdp file. However, the peptide still moves out of the box and go through to
the other side of the box. Is there any method that ca
Hi
I checked again with Gromacs 4.0.7 and I find that I have a problem
with make_edi when I use eigenvec.trr files generated using g_covar
-nofit. I use the -nofit option because the data was already fit to a
reference structure
using trjconv -fit rot+trans.
I end up with a segmentation fau
Dear Berk,
Yes the system is stable and the small velocity appears only at step 0 as
you said.
This looks fine now, Thanks a lot for you continuous support
Thanks very much.
Srinivas.
On Mon, Apr 26, 2010 at 7:43 AM, Berk Hess wrote:
> Hi,
>
> So the system seems to be stable now?
>
> The wa
Hi,
So the system seems to be stable now?
The water molecules might get a very small velocity, because constraints are
always applied.
If your starting coordinates do not have full precision (e.g. gro or pdb), a
minor correction
and thus velocity will occur at step 0 only. This should not be a
Please keep all Gromacs-related correspondence on the gmx-users list. I am not
a private tutor, and you stand a much higher probability of receiving a useful
response by contacting the community. Further, discussions are archived so that
others can benefit from the questions and answers.
B
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