Dear Abraham,
Thanks for your email. I have already read the manual to solve the problem but
I wasn't successful.
I need little more detailed answer to solve the problem.
By the way, here is the full command line for which I got the error.
$ pdb2gmx -f CYP.pdb -o CYP_CHARMM.pdb -p
On 20/04/2012 4:38 PM, Sundar Jubilant wrote:
Dear Abraham,
Thanks for your email. I have already read the manual to solve the
problem but I wasn't successful.
That's good to say (particularly the first time you post a request for
help, else you'll just get told to go and read), but is
Dear Dr. Abrahams,
I tried to re-create the issue per another e-mail and someone has since fixed
the problem as it gives no errors now? I wish I could say what the problem
was, but as I dint fix it I have no clue.
The origional command was:
qsub -M stephan.watk...@insel.ch -cwd -V -l
Dear All,
A question about data analysis. When Generating raw .xvg files of energies I
have found say 3-4 points out of 2000 (per run 11 total) is erroneous.
something like
20.43534
21.7657
22.212
-34.88
23.680
Something like that.
Now is there a routine in handling these? I
Dear Abraham,
I am ignoring hydrogens for the protein residues since I am not sure if the
Gromacs has an option to ignore hydrogen only for pretein residues but not for
the heme complexed with it.
One of my colleagues suggested to treat the Heme as an ligand not as a part of
the protein to
On 20/04/2012 7:21 PM, lloyd riggs wrote:
Dear Dr. Abrahams,
I tried to re-create the issue per another e-mail and someone has since fixed
the problem as it gives no errors now? I wish I could say what the problem
was, but as I dint fix it I have no clue.
The origional command was:
qsub
AFAIK this factor isn't included in g_wham. Think i tested this some
years ago with an older GROMACS version.
If one looks into the 'gmx_wham.c' and searches for 'ln' one finds it
only in the comments for the gaussian random numbers.
Greetings
Thomas
Hi all
According to some references
1)
On 20/04/2012 7:33 PM, Sundar Jubilant wrote:
Dear Abraham,
I am ignoring hydrogens for the protein residues since I am not sure
if the Gromacs has an option to ignore hydrogen only for pretein
residues but not for the heme complexed with it.
No, there is no ability to ignore them
Dear Abraham,
How would it work if I remove the hydrogen atoms that I wish to ignore from my
input co-ordinate file? The pdb2gmx tries to add the missing hydorgen atoms for
which the .hdb doesn't have information.
In my case here, I can consider heme as a ligand instead of having it as
On 20/04/2012 9:02 PM, Sundar Jubilant wrote:
Dear Abraham,
How would it work if I remove the hydrogen atoms that I wish to ignore
from my input co-ordinate file? The pdb2gmx tries to add the missing
hydorgen atoms for which the .hdb doesn't have information.
You've never actually told us
lloyd riggs wrote:
Dear All,
A question about data analysis. When Generating raw .xvg files of energies I
have found say 3-4 points out of 2000 (per run 11 total) is erroneous.
something like
20.43534
21.7657 22.212 -34.88 23.680
Something like that.
Where are these data from, and
Hi Gromacs users,
My invocation of mdrun, using 8 processors and the following mdp file:
title = Alkanethiol SAM MD
; Run parameters
integrator = md; leap-frog integrator
nsteps = 50; 25 * 40 = 1000 ps, 1 ns (actually .2ns
now)
dt =
Dear Justin,
Dont panic.
1) there in cyclic happening at 1/4 the entire run but offset by 2-6
picosecounds between runs.
2) There calculated PMF but the data comes from the origional pullf.xvg files
generated if I look at each point (same thing a - or low pullf point.)
-This is precluding
Dear gromacs users,
I run a REMD simulation 20ns long, enabling free energy and using a
different init_lambda value for each replica and using gromacs 4.5.3.
I run the simulation on a cluster equipped with torque queue management.
1) I used the following command in the submission script:
lloyd riggs wrote:
Dear Justin,
Dont panic.
Why would I panic? It's not my data are strange ;)
1) there in cyclic happening at 1/4 the entire run but offset by 2-6
picosecounds between runs.
2) There calculated PMF but the data comes from the origional pullf.xvg files
generated if I
This sounds to me like a periodicity issue. Were these runs conducted
with
pull_geometry = distance? If so, were the COM distances always less
than half
of the box vector along the restrained dimension(s)? Are you running with
NPT?
If the answer to any or all of these is yes,
Hi,
I am wondering how the fourierspacing parameter corresponds to fourier_nx,
fourier_ny, and fourier_nz. The manual
(http://manual.gromacs.org/current/online/mdp_opt.html#ewald) says, For
ordinary Ewald the spacing times the box dimensions determines the highest
magnitude to use in each
On Fri, 2012-04-20 at 10:33 -0400, Andrew DeYoung wrote:
Hi,
I am wondering how the fourierspacing parameter corresponds to fourier_nx,
fourier_ny, and fourier_nz. The manual
(http://manual.gromacs.org/current/online/mdp_opt.html#ewald) says, For
ordinary Ewald the spacing times the box
On 21/04/2012 12:33 AM, Andrew DeYoung wrote:
Hi,
I am wondering how the fourierspacing parameter corresponds to fourier_nx,
fourier_ny, and fourier_nz. The manual
(http://manual.gromacs.org/current/online/mdp_opt.html#ewald) says, For
ordinary Ewald the spacing times the box dimensions
Hi Neeru,
No, unfortunately I don't know much about conformational flooding, or
PLUMED. My own research has focused more on the path sampling family.
PLUMED questions come up here and there on this list, so it seems
like there are at least a few other people using it.
MZ
On Thu, Apr 19, 2012
Hi Florian and Mark,
Thank you for your time!
I am actually using (fourier_nx, fourier_ny, fourier_nz) ~ (14, 14, 125).
This is what a colleague who has recommended, although she is using a
different (somewhat slower) MD package. One question, if you have time. In
that other code, one
On Fri, 2012-04-20 at 11:35 -0400, Andrew DeYoung wrote:
Hi Florian and Mark,
Thank you for your time!
I am actually using (fourier_nx, fourier_ny, fourier_nz) ~ (14, 14, 125).
This is what a colleague who has recommended, although she is using a
different (somewhat slower) MD package.
On 21/04/2012 1:35 AM, Andrew DeYoung wrote:
Hi Florian and Mark,
Thank you for your time!
I am actually using (fourier_nx, fourier_ny, fourier_nz) ~ (14, 14, 125).
This is what a colleague who has recommended, although she is using a
different (somewhat slower) MD package. One question, if
Hi Mark and Florian,
Thank you kindly!
My colleagues and I are actually using going to use the plain Ewald method
in Gromacs. We have a slab geometry and two capacitor plates. In all cases
we use the Berkowitz dipole correction (ewald_geometry = 3dc) to obtain
pseudo 2-D summation. We have
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