XAvier Periole wrote:
One solution would be to use tabulated potential for which the
analytical form does not matter.
Uh, sure, but the shape is still changing with different atom types. Am
I missing something?
Mark
hong bingbing wrote:
Dear all,
Has anyone tried to use 2 van de Waals in
Yes, you are right! Indeed once I implement the shift scheme in the
table, the problem was solved immediately! Thank you so much for your
help!
Here, I want to include what I did just in case in future, someone has
a similar problem:
1. As David said, run a 1 step MD with -debug 1 to generate shi
Command lines that you use? Contents of the index files? Contents of the
output files?
Catch ya,
Dr Dallas Warren
Pharmacy and Pharmaceutical Sciences
Monash University
A polar bear is a Cartesian bear that has undergone a polar transformation
-Original Message-
From: gmx-users-bou
Zhe Wu wrote:
Dear David,
Thank you so much for your reply! I did try to use nstlist = -1 and I
still cannot solve the energy drifting problem. And you can see my
problem in more detail from the following link:
http://lists.gromacs.org/pipermail/gmx-users/2009-December/047299.html
And you menti
Dear David,
Thank you so much for your reply! I did try to use nstlist = -1 and I
still cannot solve the energy drifting problem. And you can see my
problem in more detail from the following link:
http://lists.gromacs.org/pipermail/gmx-users/2009-December/047299.html
And you mentioned I should us
Zhe Wu wrote:
I agree with that. But I don't know why, when using tabulated
potential, I cannot even get a box of LJ particles to have energy
conservation in NVE. Anyone has some idea?
do you use shifted VdW and nstlist = 1 or nstlist = -1?
Zhe
On Tue, Dec 8, 2009 at 3:52 AM, XAvier Periole
Hi Justin
Thanks for the suggestions. However, I don't really want to stop the
molecule moving into the next image-I start off with an alkyl chain
where a large portion of the structure overlaps the pbc.
i.e C1-C2-C3 \\ C4-C5-C6
where || is the unit cell boundary. To see the whole alkyl c
Jennifer Williams wrote:
Hi Justin
Thanks for the suggestions. However, I don't really want to stop the
molecule moving into the next image-I start off with an alkyl chain
where a large portion of the structure overlaps the pbc.
i.e C1-C2-C3 \\ C4-C5-C6
where || is the unit cell boundary
Dear Jenny,
You can do this directly in VMD, using the Periodic tab under
Graphics->Representations.
Ran
Jennifer Williams wrote:
>
>
> Hello,
>
> I am trying to find a way around a visualisation problem I am having
> in VMD. Some of my molecules go over periodic boundary conditions
> meaning th
Jennifer Williams wrote:
Hello,
I am trying to find a way around a visualisation problem I am having in
VMD. Some of my molecules go over periodic boundary conditions meaning
that bonds sometimes appear missing when looking at movies (I am trying
to fix this using wrap, unwrap and join in
Hello,
I am trying to find a way around a visualisation problem I am having
in VMD. Some of my molecules go over periodic boundary conditions
meaning that bonds sometimes appear missing when looking at movies (I
am trying to fix this using wrap, unwrap and join in VMD but as yet no
luck
I agree with that. But I don't know why, when using tabulated
potential, I cannot even get a box of LJ particles to have energy
conservation in NVE. Anyone has some idea?
Zhe
On Tue, Dec 8, 2009 at 3:52 AM, XAvier Periole wrote:
>
> One solution would be to use tabulated potential for which the
> Stefan Hoorman wrote:
> > I am trying to analyse the tilt of my helix with g_helixorient, but all
> > analysis come back as a straight line in 0. I have supplied
> > g_helixorient with the index file containing all carbon alpha atoms of a
> > single helix but simply cannot obtain anything more th
Jennifer Williams wrote:
Hello,
I have a general question re the PRODRG server used to create topologies
for gromacs.
Using PRODRG for a simple alkane I get:
[ dihedrals ]
; ai aj ak al fuc0, c1, m, ...
4 3 2 1 1 0.05.9 3 0.05.9 3 ; dih CAG
CAE CAC
Hello,
I have a general question re the PRODRG server used to create
topologies for gromacs.
Using PRODRG for a simple alkane I get:
[ dihedrals ]
; ai aj ak al fuc0, c1, m, ...
4 3 2 1 1 0.05.9 3 0.05.9 3 ; dih CAG CAE CAC
The dihedrals created are
leila karami wrote:
Hi
I want to use g_energy command.
what means of 14 in LJ-14 or coulomb-14?
Any help will highly appreciated!
Please read the manual, especially sections regarding "1-4 interactions."
-Justin
--
Justin A. Lemkul
Ph.D. Can
Hi
I want to use g_energy command.
what means of 14 in LJ-14 or coulomb-14?
Any help will highly appreciated!
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please
leila karami wrote:
Hi
what keyword is used for computation of DNA bending angle during md
simulation?
There is none. Please read the manual for analysis tools that may be useful,
i.e. g_angle, g_principal, etc.
-Justin
Any help will highly appreciated!
--
==
You haven't addressed any of the comments or questions I posted earlier:
http://lists.gromacs.org/pipermail/gmx-users/2009-December/047294.html
When asking for free help, demonstrate that you're willing to take the advice
you're given, and if that fails, state what problems remain. Otherwise,
Henry Ynag wrote:
Hello everyone,
I am quite new to gromacs. I would like to know how can I calculate the
area per lipid for my simulations. I am running simulations with 128
DMPC lipid bilayer. I have the output of 30 ns simulations. Also how
can i make a graph with this output.
Plot
Henry Yang wrote:
Hello Jon,
Thnx. One more question. I have the output of every 10 ns simulation
over 50 ns. For every 10 ns simulation step I have the .xvg file . Is
there any way in xmgrace so that I can concatenate all the .xvg file
from 0 to 50 ns simulation and show them one xmgrace g
quot;
>
> Hello everyone,
>
> I am quite new to gromacs. I would like to know how can I calculate the
> area per lipid for my simulations. I am running simulations with 128 DMPC
> lipid bilayer. I have the output of 30 ns simulations. Also how can i make
> a graph with
Hi
what keyword is used for computation of DNA bending angle during md
simulation?
Any help will highly appreciated!
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
P
Hello Jon,
Thnx. One more question. I have the output of every 10 ns simulation over 50
ns. For every 10 ns simulation step I have the .xvg file . Is there any way in
xmgrace so that I can concatenate all the .xvg file from 0 to 50 ns simulation
and show them one xmgrace graph
Thanks again
Hen
>From the command line you can type xmgrace file1.xvg file2.xvg (where file1
and file2 are the filenames!).
Jon
2009/12/8 Henry Yang
> Hello everyone,
>
> I am also new to xmgrace. I have two .xvg file which I have got from the
> simulation data analysis. How can I open both of them in one xmg
Hello everyone,
I am also new to xmgrace. I have two .xvg file which I have got from the
simulation data analysis. How can I open both of them in one xmgrace graph
with two distinct color? How can I proceed with the comand?
I know this is very basic but I have to learn!
Pls give me response.
One solution would be to use tabulated potential for which the
analytical form does not matter.
On Dec 8, 2009, at 4:29 AM, Mark Abraham wrote:
hong bingbing wrote:
Dear all,
Has anyone tried to use 2 van de Waals interaction types in one
system? For example, the system includes two compone
Hello everyone,
I am quite new to gromacs. I would like to know how can I calculate the area
per lipid for my simulations. I am running simulations with 128 DMPC lipid
bilayer. I have the output of 30 ns simulations. Also how can i make a graph
with this output.
Any help!
Henry
Biochemist
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