Hi,
Very sporadically and also with high frequent,
The job I submitted only running without writing (this job is not un-started
one, mainly one I stopped and rerun).
Before I thought I did not wait long enough, such as hours, but seriously
after 3 or 8 hours, still running not writing.
I ssh
Hi,
It works now.
Not write (just based on guess) might
the md.log step such as is 1114
while use thread I noticed the actually run step started from 11135000
so I run until it can write to the md.log
then switch to 1 node to run for a while,
then switch to more nodes.
But there might be
Hi All,
I have few questions regarding REMD simulation.
I assume REMD works in the following way: Each replica starts with a given
temperature and the temperature of each replica changes along the simulation
(as described in Sugita and Okamoto publication, 1999). Then demux.pl and
trjcat collect
Dear Michael,
First I want to say thank you very much... for posting you questions here.
I can't help you with this but I wish you Good Luck and that you will find your
answers soon!
Best wishes,thanks again,
Gal :)
Date: Sun, 18 Sep 2011 14:35:43 +0300
From: mikel...@gmail.com
To:
Hi,
in the GROMACS implementation of REM the trajectories are exchanged not
the temperatures. The temperatures are kept constant. As well as the
description of the Okamoto paper cited by GROMACS
Basti
On 09/18/2011 01:35 PM, michael zhenin wrote:
Hi All,
I have few questions regarding REMD
Hi all,
I ran g_energy in order to calculate the LJ energy between a pip2
(Phosphatidylinositol
4,5-bisphosphate) molecule and the solvent using GROMACS 4.0.7. the pip2
molecule is very polar and the avg. coulomb energy value I got between the
ligand and solvent was ~ 3100 KJ. The solvent
On 19/09/2011 1:13 AM, Gideon Lapidoth wrote:
Hi all,
I ran g_energy in order to calculate the LJ energy between a pip2
(Phosphatidylinositol 4,5-bisphosphate) molecule and the
solvent using GROMACS 4.0.7. the pip2 molecule is very polar and the
avg. coulomb energy value I got between the
On 18/09/2011 9:35 PM, michael zhenin wrote:
Hi All,
I have few questions regarding REMD simulation.
I assume REMD works in the following way: Each replica starts with a
given temperature and the temperature of each replica changes
along the simulation (as described in Sugita and Okamoto
Hi Gromacs Users,
Can anyone explain me why in g_bond the distance is takes = 3.5nm. It is
said that it comes from the first minimum o RDF of Oxygen atoms in SPC water
model. I am sorry, but I just do not catch this. Thank you in advance.
Steven
--
gmx-users mailing list
On 19/09/2011 2:02 AM, Steven Neumann wrote:
Hi Gromacs Users,
Can anyone explain me why in g_bond the distance is takes = 3.5nm.
If you mean g_hbond, and are using units incorrectly, 0.35nm would be a
characteristic distance cut-off for deciding whether a hydrogen bond
might exist
It
On Sun, Sep 18, 2011 at 5:07 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 19/09/2011 2:02 AM, Steven Neumann wrote:
Hi Gromacs Users,
Can anyone explain me why in g_bond the distance is takes = 3.5nm.
If you mean g_hbond, and are using units incorrectly, 0.35nm would be a
Steven Neumann wrote:
On Sun, Sep 18, 2011 at 5:07 PM, Mark Abraham mark.abra...@anu.edu.au
mailto:mark.abra...@anu.edu.au wrote:
On 19/09/2011 2:02 AM, Steven Neumann wrote:
Hi Gromacs Users,
Can anyone explain me why in g_bond the distance is takes = 3.5nm.
If
Hi Mark,
I don't quite understand what it follows only one [defaults] section can
exist in an entire topology.
Then how to specify different fudge values for different subsets of
non-bonded interactions?
When defining new atom types, should I always use 'new' atomtypes names? For
example, if
Yun Shi wrote:
Hi Mark,
I don't quite understand what it follows only one [defaults] section
can exist in an entire topology.
Then how to specify different fudge values for different subsets of
non-bonded interactions?
When defining new atom types, should I always use 'new' atomtypes
On Sun, Sep 18, 2011 at 5:52 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Steven Neumann wrote:
On Sun, Sep 18, 2011 at 5:07 PM, Mark Abraham
mark.abra...@anu.edu.aumailto:
mark.abra...@anu.edu.**au mark.abra...@anu.edu.au wrote:
On 19/09/2011 2:02 AM, Steven Neumann wrote:
Steven Neumann wrote:
On Sun, Sep 18, 2011 at 5:52 PM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
Steven Neumann wrote:
On Sun, Sep 18, 2011 at 5:07 PM, Mark Abraham
mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au
On Sun, Sep 18, 2011 at 7:25 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Steven Neumann wrote:
On Sun, Sep 18, 2011 at 5:52 PM, Justin A. Lemkul jalem...@vt.edumailto:
jalem...@vt.edu wrote:
Steven Neumann wrote:
On Sun, Sep 18, 2011 at 5:07 PM, Mark Abraham
Hello all,
I'm trying to pull two peptides (coordinates are from their dimer crystal
structure) apart using the distance option for the pull geometry and harmonic
potential using GMX 4.5.3 using OPLS-AA to define the protein and tip3p for the
water model with NaCl used @ 140 nM for ions. The
Robert Dole wrote:
Hello all,
I'm trying to pull two peptides (coordinates are from their dimer
crystal structure) apart using the distance option for the pull geometry
and harmonic potential using GMX 4.5.3 using OPLS-AA to define the
protein and tip3p for the water model with NaCl used @
Does not really matter which one you load up, just one towards the end of the
trajectory probably so you can be sure it is selected from the equilibrium
state of the system.
Then type 2 when over the display window with VMD, then click on two atoms.
VMD will then display a line between the
Hello,
I would like to manually place a counterion into my system with the
genion command for which I am pretty sure I will need an index file. My
question
is how to properly select the specific water atoms / or SOL residue(?) number
(that I get from my pdb or gro file) so that
Marc Charendoff wrote:
Hello,
I would like to manually place a counterion into my system with
the genion command for which I am pretty sure I will need an index file.
My question is how to properly select the specific water atoms / or SOL
residue(?) number (that I get from my
Hi,
I embedded my protein of interest into a DMPC membrane by the g_membed tool
with the following command:
g membed -f input.tpr -p system.top -n index.ndx -xyinit 0.1 -xyend 1.0 -nxy
1000 -zinit 1.1 -zend 1.0 -nz 100
I then energy minimized the resultant structure for 1 ns before the
On 19/09/2011 9:42 AM, Sweta Iyer wrote:
Hi,
I embedded my protein of interest into a DMPC membrane by the g_membed
tool with the following command:
g membed -f input.tpr -p system.top -n index.ndx -xyinit 0.1 -xyend
1.0 -nxy 1000 -zinit 1.1 -zend 1.0 -nz 100
I then energy minimized the
Unfortunately genbox will put waters anywhere there is a space, including
inside the membrane. This can easily be fixed by making a script to remove
waters that are z +/- ~2 nm from the membrane center (you should run
g_density on the system to figure out the optimal distance filter). You can
Does anyone know where I can find opls-aa parameters for strange peptide
terminal groups, such as the formyl N-terminus and ethanolamine C-terminus
of gramicidin A? I know for charmm you can auto-generate these using
swissparam but I don't know of any equivalent for opls.
Thanks,
--
Michael Daily wrote:
Unfortunately genbox will put waters anywhere there is a space,
including inside the membrane. This can easily be fixed by making a
script to remove waters that are z +/- ~2 nm from the membrane center
(you should run g_density on the system to figure out the optimal
Also it is possible that there might be a problem with setting up the
membrane. Have you tried running the membrane without protein?
-Shay
On Sep 19, 2011 3:32 AM, Justin A. Lemkul jalem...@vt.edu wrote:
Michael Daily wrote:
Unfortunately genbox will put waters anywhere there is a space,
I met the similar problem before, sometimes my job writes output, sometimes
not. My cluster administrator fixed the problem and they told me that there
were some problem at some compute nodes which my job unfortunately was
dispatched to.
Jianguo
From: lina
Hi Mark and Justin,
I think I should be more specific here. So i.e., I want to study the
interaction between a protein receptor and a carbohydrate ligand with MD
simulation, and I plan to use ff99sb for protein while glycam06 for
carbohydrate.
Since the two force fields are parameterized using
On Mon, Sep 19, 2011 at 11:31 AM, Jianguo Li ljg...@yahoo.com.sg wrote:
I met the similar problem before, sometimes my job writes output, sometimes
not. My cluster administrator fixed the problem and they told me that there
were
some problem at some compute nodes which my job unfortunately
31 matches
Mail list logo
