Dear Gmx-users,
I created a box size 4 4 2 and named layer.gro. Then "genconf" was
used to doulble this box:
genconf -f layer.gro -o 2layers.gro -nbox 1 1 2 -dist 0 0 8
However, the copied box has the same direction as the original box.
Could you please help me to rotate 180 degrees the copied one
On 17/07/2012 4:16 PM, tarak karmakar wrote:
Dear All,
I want to opt for the rhombic dodecahedron box in my simulation of a
protein. I am using the following command to select the type of the
box
"editconf -f test.gro -o test_box.gro -c -d 1.2 -bt dodecahedron"
but after this if I'm seeing this
Dear All,
I want to opt for the rhombic dodecahedron box in my simulation of a
protein. I am using the following command to select the type of the
box
"editconf -f test.gro -o test_box.gro -c -d 1.2 -bt dodecahedron"
but after this if I'm seeing this protein system within the box in VMD
but its n
On 7/16/12 5:42 PM, Manikam Sadasivam Saravanan wrote:
Hi,
I am a new user to Gromacs, just started exploring it since 3 months, Thanks
to Justin, In-fact i learned a lot form his tutorial using KALP protein in
dppc.
Currently I am working with simulation of Membrane protein in a popc
bilayer
Hi,
I am a new user to Gromacs, just started exploring it since 3 months, Thanks
to Justin, In-fact i learned a lot form his tutorial using KALP protein in
dppc.
Currently I am working with simulation of Membrane protein in a popc
bilayer, its a complete membrane protien which lies in one of the
On 7/16/12 10:59 AM, Andrew DeYoung wrote:
Hi,
If you have time, I'm wondering if you can please help me to think through a
problem that I seem to be having with g_hbond. I am looking for a way to
list the _individual_ hydrogen bonds as a function of time, by indices --
more than just determi
Hi,
If you have time, I'm wondering if you can please help me to think through a
problem that I seem to be having with g_hbond. I am looking for a way to
list the _individual_ hydrogen bonds as a function of time, by indices --
more than just determining the number of hydrogen bonds at every time
On 7/16/12 10:39 AM, Giovani Mancini wrote:
Dear Justin,
Thank you very much for your immediate response to my e-mail.
I am trying to conduct umbrella sampling simulations of a molecule into a lipid
bilayer (DLPC) along the z-axis. As a reference, I used your tutorial which is
well-written
Dear Justin,
Thank you very much for your immediate response to my e-mail.
I am trying to conduct umbrella sampling simulations of a molecule into a lipid
bilayer (DLPC) along the z-axis. As a reference, I used your tutorial which is
well-written and provide useful information of how to set up
On 7/16/12 10:25 AM, Giovani Mancini wrote:
Dear Gromacs users,
I just read the tutorial by Justin Lemkul about umbrella sampling simulations
along z-axis. My question is whether we need cylindrical confinement of the
molecule that is pulling away from a reference molecule.
Thanks in advance
Dear Gromacs users,
I just read the tutorial by Justin Lemkul about umbrella sampling simulations
along z-axis. My question is whether we need cylindrical confinement of the
molecule that is pulling away from a reference molecule.
Thanks in advance
Best regards,
Giovani
--
gmx-users mailing l
On 13/07/2012 7:05 PM, Shima Arasteh wrote:
Dear gmx users,
My system is composed of a protein and water. I am working with CHARMM36 and
the current version of Gromacs, 4.5.5.
For NVT equilibration , I get this error:
"Software inconsistency error:
Some interactions seem to be assigned mult
On 13/07/2012 9:56 PM, J Benet wrote:
Hi, I would like to know if it's possible to perform an NVT simulation but
letting the box shape to fluctuate.
Probably possible, but not implemented. What physical conditions would
it model?
Mark
--
gmx-users mailing listgmx-users@gromacs.org
http:/
On 7/16/12 7:19 AM, Inon Sharony wrote:
Good afternoon.
g_traj has the option to output position coordinates (-ox) OR velocity
coordinates (-ox) from an input trajectory file. The former can even be
output to a trajectory file format, trr/trj/cpt (-oxt). I would like to
res
I thought setting tau_t=0 for some of the groups means that they're not
coupled. That is tau_t would in fact be infinite, but that would be more
difficult to input, whereas if tau_t were actually equal to zero the
situation (as you described it) would lack physical significance...
Since only the No
Correction -- in the first sentence:
"... velocity coordinates (-ov) ..."
Inon Sharony J+N+W+N% ShR+W+N+J+
[1]http://atto.TAU.ac.IL/~InonShar
+972-3-640-7634
On 07/16/2012 02:19 PM, Inon Sharony wrote:
Good afternoon.
g_traj has the option to output position coordinates (
Good afternoon.
g_traj has the option to output position coordinates (-ox) OR velocity
coordinates (-ox) from an input trajectory file. The former can even be
output to a trajectory file format, trr/trj/cpt (-oxt). I would like to
restart a simulation using a separate set of MD para
On 7/16/12 5:36 AM, Raj wrote:
Hi all,
It may be naive but I would like to get some clear explanation in SMD ( COM
pulling) reg. The question is, Before performing the COM-pulling (incase of
protein ligand complex) do we need to position restrain the ligand using
genrestr and then add the to
Hi all,
It may be naive but I would like to get some clear explanation in SMD ( COM
pulling) reg. The question is, Before performing the COM-pulling (incase of
protein ligand complex) do we need to position restrain the ligand using
genrestr and then add the topology to the topol.top file. If not
19 matches
Mail list logo
