Makoto Yoneya wrote:
Dear GROMACS users:
I found the following in ML archive about the box vectors entry in "gro"
file.
doing:
% editconf -f -o -bf tric -box a b c -angles bc ac
ab
the last line of out.gro looks like:
1.12020 0.92620 6.259008 0.0 0.0 0.0 0.0 -0.99134
0
Hello Dr. David,
Now it is clear to me about the 30 cutoff angle. In some papers the
Donor-Hydrogen-Acceptor angle is mentioned as 120 & anything above it till the
linear angle (180). In the latest paper of Prof Gunsteren in Eur Biophys J on
Melittin there he h
Hi,
I want to do a simulation with tabulated VDW potential. Can anyone
please tell me what should be the final limit of 'r'. In the manual it
is written as rc + 1.0. Say if my 'rc' is 4.29 nm. And interval is
0.002nm . Then what should be my limit.
--
This message has been scanned for viruses
Dear GROMACS users:
I found the following in ML archive about the box vectors entry in "gro"
file.
>> doing:
>> % editconf -f -o -bf tric -box a b c -angles bc ac
>> ab
>>
>> the last line of out.gro looks like:
>>1.12020 0.92620 6.259008 0.0 0.0 0.0 0.0 -0.99134
>> 0.000
jayant james wrote:
Hi!
During simulations for distance restraints to kick in, is it necessary
to specify disre = simple even after it is defined as DDISRES in the
pr.mdp file?
Thanks
Jayant
Ititle =
cpp = /usr/bin/cpp
define = -DDISRES -DPOSRES
.
Hi!
During simulations for distance restraints to kick in, is it necessary to
specify disre = simple even after it is defined as DDISRES in the pr.mdp
file?
Thanks
Jayant
Ititle =
cpp = /usr/bin/cpp
define = -DDISRES -DPOSRES
. .
. .
. .
-.-
Jayasundar Ja
Zoltan Varga wrote:
Hi,
Actually gnuplot can plot the xvg files without any modification. It
skips all the lines in the file which is not compatible with the
command: u 1:2
Interesting, that's true. I'll update the wiki. If one is happy using
the "using" approach then that works, but for mo
huan wrote:
hello gromacs users..
i had read a journal which used Gromacs program in the
project. I am wondering how to obtain the number of
aggregates vs time graph and the size distribution of
aggregates graph??
g_clustsize might help
thanks for the help.
__
hello gromacs users..
i had read a journal which used Gromacs program in the
project. I am wondering how to obtain the number of
aggregates vs time graph and the size distribution of
aggregates graph??
thanks for the help.
__
hello gromacs users..
i had read a journal which used Gromacs program in the
project. I am wondering how to obtain the number of
aggregates vs time graph and the size distribution of
aggregates graph??
thanks for the help.
_
Hi,
Actually gnuplot can plot the xvg files without any modification. It skips all
the lines in the file which is not compatible with the command: u 1:2
The problem is the missing word about how to draw the data. Maybe you have also
recognized it meanwhile. In the correct form:
>plot "rmsf.xvg"
Florian Haberl wrote:
take a look on your data file
less rmsf.xvg
first 12 lines or so are without data. It is the header for xmgrace, so you
have to ignore them your delete out of the file.
You can also analyse the data with the flag -noxvgr, than it will be written
without xmgrace heade
Robert Johnson wrote:
Hello Pascal,
I'm not sure I can really comment on (1), but the reason why your
energy gap decreases in (2) is because the energy fluctuations in your
system increase as you raise the temperature. For example, at low
temperatures your potential energy distributions will be s
Hello Pascal,
I'm not sure I can really comment on (1), but the reason why your
energy gap decreases in (2) is because the energy fluctuations in your
system increase as you raise the temperature. For example, at low
temperatures your potential energy distributions will be sharply
peaked about the
Andy Shelley wrote:
Hello,
I am trying to model heat flux across a carbon nanotube and was planning
on using the annealing function to set and hold a temperature difference
across the tube to create a heat flux. I was wondering if anyone had
some thoughts on short comings with this idea or a
Hello,
I am trying to model heat flux across a carbon nanotube and was planning on
using the annealing function to set and hold a temperature difference across
the tube to create a heat flux. I was wondering if anyone had some thoughts
on short comings with this idea or a better way to model the
Dear community,
I am performing some REMD tests with the trp-cage peptide. In order to figure
out the optimal temperature distribution ensuring similar exchange probabilities
at every temperature, I have performed short MD runs at increasing temperatures,
with a run every 5K from 300K to 500K. If
Hello!
Please note that xmgrace and gunplot are two different programs and as
such work in different ways, for example in terms of what types of
input and output they expect. The xvg-files that Gromacs produces are
indended for xmgrace, and will not work out-of-the-box with gnuplot.
There
Hi,
On Tuesday, 6. May 2008 15:07, s lal badshah wrote:
> Dear Mark,
> Hi ! Currently I tried to install xmgrace but the toolbar menue is not
> shown on window screen so I am using gnuplot for analysis as I have little
> know how about unix/linux.Please set to me the following. [EMAIL
> PROTECTE
Dear Mark,
Hi ! Currently I tried to install xmgrace but the toolbar menue is not shown on
window screen so I am using gnuplot for analysis as I have little know how
about unix/linux.Please set to me the following.
[EMAIL PROTECTED]:~> cd project
[EMAIL PROTECTED]:~/project> ls
#bfac.pdb.1# con
sharada wrote:
Hi,
Thank you all for the response, Yes, the backbone of my protien does
not have the required -Hydrogens for the program to calculate the
hydrogen bonds. The option 6 (Mainchain +H) worked for me. Still I am
not clear as to what exactly are cut off angle 30 degrees and cut-
Hi,
Thank you all for the response, Yes, the backbone of my protien does not have
the required -Hydrogens for the program to calculate the hydrogen bonds. The
option 6 (Mainchain +H) worked for me. Still I am not clear as to what exactly
are cut off angle 30 degre
Hi,
Where did you get this 10% number?
I would expect that for Gromacs the performance is linear with the clock
frequency
and the FSB does not matter much. Thus the difference is only 5%.
I would rather have 20% more nodes.
Berk.
> Date: Mon, 5 May 2008
This book is out now:
Molecular Modeling of Proteins
# Hardcover: 396 pages
# Publisher: Humana Press; 1 edition (February 19, 2008)
# Language: English
# ISBN-10: 1588298647
# ISBN-13: 978-1588298645
Here is a list of contents:
Methodology
1 Molecular dynamics simulations
Erik R. Lindahl
2 Mo
1) You need to include ions.itp in your topology file:
#include ions.itp
2) Make sure, you include the correct name for the atom in the systems section
of your topology file:
For gromos96 forcefield variants this is 'CL-'
Good luck
Andreas
> -Original Message-
> From: [EMAIL PROTECTED
Hi,
You have not used the right command for adding the CL- ion to your system.
Before adding/doing your simulation you must go through the manual and
useful tutorial of John E. Kerrigan. Use genion command to add the charged
ions.
regards
anil
-
(¨`•.•´¨) Always
`•.¸(¨`•.•´¨) Keep
(¨`•.•´¨)¸.•´ S
On Tue, 6 May 2008 13:17:29 +0530 (IST)
[EMAIL PROTECTED] wrote:
Dear Users
When I try adding charges (negative charges by adding Cl), using the command
/opt/gromacs/bin/grompp_mpi -np 32 -f em_cc.mdp -po det_em2.mdp -c
1A92_m1_neu.gro -p 1A92_m1.top -o 1A92_m1_em.tpr
it gives me the followin
Dear Users
When I try adding charges (negative charges by adding Cl), using the command
/opt/gromacs/bin/grompp_mpi -np 32 -f em_cc.mdp -po det_em2.mdp -c
1A92_m1_neu.gro -p 1A92_m1.top -o 1A92_m1_em.tpr
it gives me the following error...
---
OK I'll use bonds 6 instead. Although I understand what "constraints =
all-bonds" means, I prefer to be sure : are bonds 6 indeed treated as
constraints ? Then, there should be no difference at all with bonds 1, if I am
right.
By the way, is there a simple way to treat all bonds but one as const
On Tue, 6 May 2008 11:07:11 +0530 (IST)
[EMAIL PROTECTED] wrote:
Dear members
I am working on simulation of certain models of protein myosin. When I use
the grompp_mpi (for position restraint), it gives me an error message as
"Fatal error: Invalid line in em.gro for atom 3642:" and the program
[EMAIL PROTECTED] wrote:
Dear members
I am working on simulation of certain models of protein myosin. When I use
the grompp_mpi (for position restraint), it gives me an error message as
"Fatal error: Invalid line in em.gro for atom 3642:" and the program is
aborted.
Could you please tell me what
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