On 3/06/2011 3:06 AM, Elisabeth wrote:
Hello all,
I am getting the error below at the very beginning of the simulation
(both serial and parallel). I am sure I did not encounter this problem
before with the same input files. This has just happened now. I really
have no clue why this is happeni
On 3/06/2011 3:42 PM, Kavyashree M wrote:
Dear users,
I wanted to ensure that the option of -pbc in trjconv is only for
visualization,
and if I do all possible calculations with the original .xtc file
there wont be any
problem.
-pbc is for any purpose you can think of. Some analyses of
Dear Sir,
I used dodecahedron for the simulation. My specific doubt was whether
do we need to modify the .xtc file using some options of -pbc like nojump,
mol, before going for analysis or we can directly go for analysis using the
raw .xtc file.
Thanking you
With regards
M. Kavyashree
>
> ---
On 3/06/2011 6:48 PM, Kavyashree M wrote:
Dear Sir,
I used dodecahedron for the simulation. My specific doubt was whether
do we need to modify the .xtc file using some options of -pbc like
nojump,
mol, before going for analysis or we can directly go for analysis
using the
raw .xtc file.
M
Hi Gromacs users,
We would like to apply strain to the system. Is this possible to do with
gromacs and if it is how?
Thank you in advance,
Deniz
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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
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Hi Justin,
> Note that the pseudo-sphere representation is for visualization
> purposes only; the triclinic cell should be the input for any simulation.
This not true. It doesn't matter which representation you use as
input. Molecules may be broken over PBC, but the topological
information is tak
Tsjerk Wassenaar wrote:
Hi Justin,
Note that the pseudo-sphere representation is for visualization
purposes only; the triclinic cell should be the input for any simulation.
This not true. It doesn't matter which representation you use as
input. Molecules may be broken over PBC, but the topo
Hi all,
I just discovered nohup for running my simulation without hangup. For
some reason using nohup wouldn't except the checksum on my previous
md.log file so I just added the -noappend option to create new files.
I'm curious, is there a way to combine the part files that emerge from
using the
Zack Scholl wrote:
Hi all,
I just discovered nohup for running my simulation without hangup. For
some reason using nohup wouldn't except the checksum on my previous
md.log file so I just added the -noappend option to create new files.
I'm curious, is there a way to combine the part files tha
Hi Justin,
I added this feature as a new issue under the Gromacs project on Redmine.
Recently I also added a Git fork with a very rudimentary version of rigid
body code. Let me know if there is anything specific you think I should
work on. Thanks a lot,
Adam
On Thu, Apr 7, 2011 at 12:58 PM, Ju
Add --with-pic when configuring fftw.
-- Josh
On Thu, 2011-06-02 at 15:16 +0800, Jianguo Li wrote:
> The error message already shows some hints. Try recompile FFTW with
> -fPIC.
> Jianguo
>
>
>
>
> __
> From: Chandan Choudhu
Hello, I'll first apologize in case that this is a common issue with
an available solution, but I have a problem running mdrun_mpi on a
rock cluster and there
is no amount of searching that I can do to find information on this
error (manual, online docs, general google search). Could someone
point
Hi,
I have a question on correlating the RMSFs with order paramters derived from
g_chi - omega or g_rotacf. Which set of order parameters would correlate well,
or should I use, with RMSFs? I used C-alpha for RMSFs.
Thanks for your insight.
Simon
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gmx-users mailing listgmx-users@gromacs.o
On 4/06/2011 3:42 AM, Christian Blouin wrote:
Hello, I'll first apologize in case that this is a common issue with
an available solution, but I have a problem running mdrun_mpi on a
rock cluster and there
is no amount of searching that I can do to find information on this
error (manual, online do
Eli:
It was a joke.
I want to clarify your relation to Moeed since he asked the SAME
question about the compression of the SAME polymer starting from the
spring of 2010, but never followed all our advices. Now, you start to
ask nearly the SAME questions about absolutely the SAME system. So, I
eve
At first, I thought the -append option of the mdrun command was great.
However, I don't think it is anymore and have actually started questioning
myself why it exists at the first place, and second, why has it become the
default option in the newest versions?
It is useless unless you run your sim
Well sometimes i run out of walltime when doing long simulations and append
helps me not to do any file management after restarting simulations from the
previous checkpoint.
On Fri, Jun 3, 2011 at 3:26 PM, Dimitar Pachov wrote:
>
> At first, I thought the -append option of the mdrun command was
Hi,
I have tried to use g_rotacf to get the rotational autocorrelation plot for a
n-h vector, and I have two questions:
1. My MD run is 20ns, but the rotacf.xvg shows only 10ns. why?
2. The plot is bottom out at 500 ps and then go back up. What does it mean
physically?
Thanks for your insight.
On 4/06/2011 8:26 AM, Dimitar Pachov wrote:
At first, I thought the -append option of the mdrun command was great.
However, I don't think it is anymore and have actually started
questioning myself why it exists at the first place, and second, why
has it become the default option in the newes
On 4/06/2011 9:02 AM, simon sham wrote:
Hi,
I have tried to use g_rotacf to get the rotational autocorrelation
plot for a n-h vector, and I have two questions:
1. My MD run is 20ns, but the rotacf.xvg shows only 10ns. why?
This can be normal for computed correlation functions. See chapter 5.
On 4/06/2011 11:27 AM, Mark Abraham wrote:
On 4/06/2011 9:02 AM, simon sham wrote:
Hi,
I have tried to use g_rotacf to get the rotational autocorrelation
plot for a n-h vector, and I have two questions:
1. My MD run is 20ns, but the rotacf.xvg shows only 10ns. why?
This can be normal for co
Hi,
I am using gromacs_4.0.7 to calculate the Scattering Intensity as a function
of scattering vectors(q) using g_rdf -sq command .
But, I found that there is no way that one can increase/decrease the grid
spacing for structure factor calculation. I tried using -bin option , but that
does not
Justin A. Lemkul wrote:
>
>
> Ryan S Davis (rsdavis1) wrote:
>> I wanted to copy a bilayer into a grid of 2x2x1 replicas. I used
>> genconf and everything seemed to work fine exept that annoying feature
>> that the command does not reorder the molecule types, so I end up with
>> a .top file lookin
Thanks everyone. It helped me in installation.
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Fri, Jun 3, 2011 at 10:36 PM, Joshua L. Phillips wrote:
> Add --with-pic when configuring fftw.
>
> -- Josh
>
> On Thu, 2011-06-02 at 15:16 +0800, Jianguo Li wrote:
> > The error message already shows
Dear Gromacs users,
I am new to essential dynamics, I have gone through
some fundamentals in PCS, the mailing list related to ED
and few publications by -
Amadei (Proteins, 17, 412-425, 1993),
a. Amadei (journal of biomolecular structure and dynamics, 13, 615, 1996)
b. Berk Hess (Physical reviews
On 4/06/2011 2:52 PM, Ryan S Davis (rsdavis1) wrote:
Justin A. Lemkul wrote:
Ryan S Davis (rsdavis1) wrote:
I wanted to copy a bilayer into a grid of 2x2x1 replicas. I used
genconf and everything seemed to work fine exept that annoying feature
that the command does not reorder the molecule typ
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