On 19/01/2012 5:39 PM, Chandan Choudhury wrote:
Dear gmx-users,
I have a simulated a system containing a linear polymer in a cubic box
with water molecules. I need to get rid of PBC effect on the system
such that I can execute my own analysis code. I intend to compute the
msd of water molec
Hi Chadan,
You should stop after your second step, removing jumps. Don't center.
And definitely don't put the system in the box, as that exactly undoes
removal of jumps.
Cheers,
Tsjerk
On Thu, Jan 19, 2012 at 7:39 AM, Chandan Choudhury wrote:
>
> Dear gmx-users,
>
> I have a simulated a system
Dear gmx-users,
I have a simulated a system containing a linear polymer in a cubic box with
water molecules. I need to get rid of PBC effect on the system such that I
can execute my own analysis code. I intend to compute the msd of water
molecules along the polymer backbone. So, when I execute my
On 19/01/2012 3:17 PM, bharat gupta wrote:
No. I am not trying to crosslink the chromophore with nay residue but
I have linked it with neighboring Valine(68) and Leucine(64) by
specifying the bonds in specbond.dat file.
You still have to go and look at residue 51 and see what is going on.
Th
No. I am not trying to crosslink the chromophore with nay residue but I
have linked it with neighboring Valine(68) and Leucine(64) by specifying
the bonds in specbond.dat file.
On Thu, Jan 19, 2012 at 12:09 PM, Peter C. Lai wrote:
> Are you crosslinking the chromophore to an atom in residue 51?
Size Zheng wrote:
Dear All,
We are doing a simulation for ice melting in Efield with thermostat. We would
like use Andersen thermostat to couple the temperature but found that it is
not implemented yet, even on the latest version of GROMACS. Is there any way
we can employ Andersen thermostat d
Dear All,
We are doing a simulation for ice melting in Efield with thermostat. We would
like use Andersen thermostat to couple the temperature but found that it is not
implemented yet, even on the latest version of GROMACS. Is there any way we can
employ Andersen thermostat directly on GROMACS
Are you crosslinking the chromophore to an atom in residue 51?
Can you generate a correct topology without the chromophore as a check?
On 2012-01-19 11:50:37AM +0900, bharat gupta wrote:
> Hi,
>
> I have been trying to attach the chromophore of GFP in charmm ff parameter
> files. The parameters
Hi,
I have been trying to attach the chromophore of GFP in charmm ff parameter
files. The parameters have been obtained from a published article. After
making the changes as per the documentation (
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field)
, I am getting follo
On 19/01/2012 2:59 AM, aiswarya.pa...@gmail.com wrote:
Hi,
Its going into the running mode but gets hang there for long hours which
generating any data in the output file. And am not able to figure out the error
file_doc. Please anyone knows what's going wrong.
No, but you should start tryin
Hi,
Its going into the running mode but gets hang there for long hours which
generating any data in the output file. And am not able to figure out the error
file_doc. Please anyone knows what's going wrong.
Thanks
Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!
Hi,
Most of those are just warnings, the only error I see there comes from
the shell, probably an error in your script.
Cheers,
--
Szilárd
On Wed, Jan 18, 2012 at 12:27 PM, aiswarya pawar
wrote:
> Hi users,
>
> Am running mdrun on gpu . I receive an error such as=
>
> WARNING: This run will g
On 18.01.2012 07:31, Ravi Kumar Venkatraman wrote:
Dear All,
I have ran a 10 ns production run for chloranil in 500 methanol solvent box. I
want to get the coordinates of solvent and solute at different time steps from
the trajectory file (*.xtc). Can anybody tell me how to extract the details
Hi,
1.method:
You can install it from Synaptic package manager.
2.method:
sudo apt-get install libfftw3-dev
Later, in gromacs directory
./configure
sudo make
sudo make install
sudo make mdrun
sudo make links
2012/1/18 Mark Abraham
> On 18/01/2012 7:30 PM, kumud agarwal wrote:
>
> Hi
>
> I have
On 18/01/2012 8:35 PM, Mr Bernard Ramos wrote:
Hi everyone!
On this page
http://manual.gromacs.org/online/g_hbond.html
there is an option -r2 when using g_hbond. What is this r2? I can't
find it in the Gromacs manual. option -a is the angle H-O-O, option -r
is the O-O distance which can be
pitheve...@free.fr wrote:
Dear all,
I'm using the option -ss to select the SS bonds I want to preserve when so
problem occur with multiple bonds possible.
The problem is that pdb2gmx asks me if I want to preserve the bound between an
atom or not. It is very difficult to do this automatically
On 18/01/2012 7:30 PM, kumud agarwal wrote:
Hi
I have been trying to install Gromacs on ubuntu.
After make command I got the following error
*/usr/bin/ld: /usr/local/lib/libfftw3f.a(alloc.o): relocation
R_X86_64_32 against `.rodata.str1.1' can not be used when making a
shared object; recompi
Rausch, Felix wrote:
Or you could use trjconv in a little script to convert the snapshots you
like to .pbd. Use the –b and –e flags to choose the respective time points.
Also see
http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts
for the use trjconv non-interactively.
Hi users,
Am running mdrun on gpu . I receive an error such as=
WARNING: This run will generate roughly 38570 Mb of data
WARNING: OpenMM does not support leap-frog, will use velocity-verlet
integrator.
WARNING: OpenMM supports only Andersen thermostat with the
md/md-vv/md-vv-avek integrators.
Dear all,
I'm using the option -ss to select the SS bonds I want to preserve when so
problem occur with multiple bonds possible.
The problem is that pdb2gmx asks me if I want to preserve the bound between an
atom or not. It is very difficult to do this automatically.
Is there a way to tell pdb2g
Hi everyone!
On this page
http://manual.gromacs.org/online/g_hbond.html
there is an option -r2 when using g_hbond. What is this r2? I can't find it in
the Gromacs manual. option -a is the angle H-O-O, option -r is the O-O distance
which can be switched to H-A by using the "-da no". Nee
Or you could use trjconv in a little script to convert the snapshots you
like to .pbd. Use the -b and -e flags to choose the respective time
points.
Also see
http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts
for the use trjconv non-interactively.
Good luck.
Von: gmx-u
Dear Tsjerk,
Thanks very much indeed for confirming this, really appreciate it. I will do as
you suggest to have a more thorough check.
Best wishes,
Huiwen
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of Tsjerk Wassenaar
Sent: Wednesday, January 18, 2012
Hi
I have been trying to install Gromacs on ubuntu.
After make command I got the following error
*/usr/bin/ld: /usr/local/lib/libfftw3f.a(alloc.o): relocation R_X86_64_32
against `.rodata.str1.1' can not be used when making a shared object;
recompile with -fPIC*
*/usr/local/lib/libfftw3f.a: c
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