Hi Peter,
> Instead of the pairs with the shortest distance a much further pair is
> selected. Although the output pair from "atm-pair.out" has a distance of more
> then 100 Angstrom the value in the file "mindist.xvg" is smaller then one
> Angstrom.
Periodic Boundary Conditions?
You mention
Bad choice of words. Did not mean to suggests there's actual program bug.
-Shay
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: Wednesday, December 02, 2009 00:46
To: Discussion list for GROMACS users
Subject
Hi Mark,
Ok here is the command line i used :-
g_angle -f after_md.trr -type dihedral -n chain1.ndx -b 800 -e 804 -all
output is
# This file was created Tue Dec 1 20:20:41 2009
# by the following command:
# g_angle -f after_md.trr -type dihedral -n chain1.ndx -b 800 -e 804 -all
#
# g_angle is
Amit Choubey wrote:
Hi Mark,
It does seem that the -all option averages the distributions.
The thing is i was confused with "the first graph is the average, the
rest are the individual angles." because when i tried it previously i
only found 2 columns which were angle and distribution.
But
Hi Mark,
It does seem that the -all option averages the distributions.
The thing is i was confused with "the first graph is the average, the rest
are the individual angles." because when i tried it previously i only found
2 columns which were angle and distribution.
But now i checked again explic
t.peter.muel...@gmx.net wrote:
Dear Shay, dear Justin, dear Gromacians
My problem is solved. I used following command
$ g_mindist -f system_onlyCa.xtc -s system_onlyCa.pdb -n system_onlyCa.ndx -o
atm-pair.out
The PDB file "system_onlyCa.pdb" had a header which seems to have confused
the coun
XunJie Yang wrote:
hello GMX users:
I am now using GMX together with FFamber, I found that the parameter files
provided by FFamber uses RB functions (described in GMX manual p62) rather than
normal dihedral function to calculate dihedral energy term. According to the
manual(p62), when using
Amit Choubey wrote:
Hi everyone,
I am trying to analyze dihedrals of molecules after a simulation. I am
able to calculate dihedral distribution at ant particular time using g
-angle and proper group using
g_angle -f after_md.trr -b 800 -type dihedral -n chain1.ndx -od dihed12
This gives me t
hello GMX users:
I am now using GMX together with FFamber, I found that the parameter files
provided by FFamber uses RB functions (described in GMX manual p62) rather than
normal dihedral function to calculate dihedral energy term. According to the
manual(p62), when using RB function for dihed
Hi everyone,
I am trying to analyze dihedrals of molecules after a simulation. I am able
to calculate dihedral distribution at ant particular time using g
-angle and proper group using
g_angle -f after_md.trr -b 800 -type dihedral -n chain1.ndx -od dihed12
This gives me the distribution at t=800
Sarah Witzke wrote:
Per the documentation, the only options that can be passed to g_saltbr are -s
and -f, so no, you cannot use any index groups.
I thought so :-(
Indeed, Mark's clever suggestion may be useful here.
There are no old xvg files in the directory. I have used "rm -r
Dear Shay, dear Justin, dear Gromacians
My problem is solved. I used following command
$ g_mindist -f system_onlyCa.xtc -s system_onlyCa.pdb -n system_onlyCa.ndx -o
atm-pair.out
The PDB file "system_onlyCa.pdb" had a header which seems to have confused the
counting of the "g_mindist" comma
Tom wrote:
> If you read this part of the manual again you will see that it discusses
> this point of 1-4 interactions for the OPLS forcefield and RB dihedrals
> (and the same as discussed for OPLS is true for the AMBER forcefields using
> RB potentials for dihedrals).
>
> Tom
>
Thanks very
Sarah Witzke wrote:
Then I run the command again with -sep to get the individual graphs of each
interaction. This is unfortunately a rather tedious exercise since very many
files are generated for all sort of charged interactions (DMPC-DMPC,
smallmolecule-smallmolecule, counterion-counterion, an
Sarah Witzke wrote:
> Dear gmx users,
>
>
>
> I'm sorry to continue an old thread - here's a summary:
>
> I have a DMPC bilayer surrounded by water and a small organic molecule with a
> deprotonated carboxylic acid. The small molecule diffuses near the membrane
> interface/into the membrane. I woul
Mark Abraham wrote:
mrshi...@gmail.com wrote:
What other input might you need for a test set? As a minor developer
and a stickler for accuracy, I would be very much interested in the
sorts of inputs your looking for, and have some ideas as well.
I'd be willing to help, as well.
There's a
Sarah Witzke wrote:
Dear gmx users,
I'm sorry to continue an old thread - here's a summary:
I have a DMPC bilayer surrounded by water and a small organic molecule with a
deprotonated carboxylic acid. The small molecule diffuses near the membrane
interface/into the membrane. I would like to
Dear gmx users,
I'm sorry to continue an old thread - here's a summary:
I have a DMPC bilayer surrounded by water and a small organic molecule with a
deprotonated carboxylic acid. The small molecule diffuses near the membrane
interface/into the membrane. I would like to calculate any formed
t.peter.muel...@gmx.net wrote:
Dear Shay, dear Gromacians
For purposes of debugging this bug you can also use the flag of g_mindist
that gives out atom pairs and see which atom pairs is it that gromacs
thinks are less the 1 angstrom.
I used the "-o atm-pair.out" option to get the atom pair
servaas skrev:
Message: 4
Date: Tue, 1 Dec 2009 13:56:21 +
From: Alan
Subject: [gmx-users] Re: amber force field in Gromacs
To: gmx-users@gromacs.org
Message-ID:
Content-Type: text/plain; charset=UTF-8
Dear Servaas,
I've been following your thread. I am the developer of acpypi and
Dear Shay, dear Gromacians
>For purposes of debugging this bug you can also use
>the flag of g_mindist that gives out atom pairs and
>see which atom pairs is it that gromacs thinks are
> less the 1 angstrom.
I used the "-o atm-pair.out" option to get the atom pairs with the minimal
distance.
Fo
Jörn-Benjamin Lenz wrote:
thanks you xavier and justin for your answers on my problem, however, i still
wonder why i could completely delete the e.g. five trr files (from an REMD
simulation on our cluster) named trajX.trr (with X = 0..4) and the
corresponding xtc files (trajX.xtc) were still wr
thanks you xavier and justin for your answers on my problem,
however, i still wonder why i could completely delete the e.g. five trr files
(from an REMD simulation on our cluster) named trajX.trr (with X = 0..4) and
the corresponding xtc files (trajX.xtc) were still written out in one of the
for
There is no problem with the rhombic dodecahedron in and of itself.
Note that editconf -d does not actually yield the -d that you ask it
to and that it errs on different sides of your request for different
box types. To prove this to yourself, run your starting structure
through editconf -d
Hi Daniel,
1a. I am confused about what is your vesicle. Is it everything that
you are showing in these images? Or perhaps it is only the cyan thing
that I can see sliced through in:
http://img109.imageshack.us/img109/8227/trajenddat.jpg
1b. I suspect that the cyan ring encircled by green
Francesco Pietra wrote:
Is anything recent to account for (and eliminate) clashes - if any -
resulting from solvating a system of protein partly immersed into a
canonical DPPC bilayer? That is, the solvation water faces three
different environments: the extracellular portion of the protein, th
Is anything recent to account for (and eliminate) clashes - if any -
resulting from solvating a system of protein partly immersed into a
canonical DPPC bilayer? That is, the solvation water faces three
different environments: the extracellular portion of the protein, the
two water layers of DPPC,
On Dec 1, 2009, at 6:33 PM, XAvier Periole wrote:
you do not need itp file. in the top you'd find the parameters for
the water.
I mean in the top file you'll find the reference to the martini??.itp
file
where the water is defined.
On Dec 1, 2009, at 6:26 PM, Francesco Pietra wrote:
I fo
you do not need itp file. in the top you'd find the parameters for
the water.
On Dec 1, 2009, at 6:26 PM, Francesco Pietra wrote:
I forgot to ask, in additio to below, where to find the .itp file for
cg water. All that I have is water.gro water.mdp water.top from the
martini web site.
--
I forgot to ask, in additio to below, where to find the .itp file for
cg water. All that I have is water.gro water.mdp water.top from the
martini web site.
-- Forwarded message --
From: Francesco Pietra
Date: Tue, Dec 1, 2009 at 6:15 PM
Subject: Re: [gmx-users] Last step before C
On Mon, Nov 30, 2009 at 5:51 PM, Justin A. Lemkul wrote:
>
>
> Francesco Pietra wrote:
>> cpp = /usr/bin/cpp
>> define = -DFLEX_SPC
>
> You're using SPC water in a coarse grain model? This doesn't make sense to
> me - an atomistic solvent with CG protein?
In order
Dear Peter,
For purposes of debugging this bug you can also use the flag of
g_mindist that gives out atom pairs and see which atom pairs is it
that gromacs thinks are less the 1 angstrom.
Another suggestion would be using the backbone and seeing if it matters any.
Regards,
-Shay
Quoting t
Ok, I guess in future I will have to make sure the box is big enough to contain
the entire vesicle in the triclinic representation. It's kind of a shame
though, as the main reason for using the rhombic dodecahedron box was to
minimize the amount of bulk solvent required.
Thanks for your help t
Jörn-Benjamin Lenz wrote:
dear users of gromacs,
i updated my gromacs from 4.0.1 to 4.0.5 and now i am facing the following
problem:
Good move, version 4.0.1 was badly broken :)
using the older version of gromacs I submitted REMD jobs to our cluster (which
also was updated from suse 10.
you can define the frequency of writing to the trr file in the mdp file.
using:
nstxout = 0
nstvout = 0
nstfout =0
should fix your problem.
On Dec 1, 2009, at 4:30 PM, Jörn-Benjamin Lenz wrote:
dear users of gromacs,
i updated my gromacs from 4.0.1 to 4.0.5 and now i am facing the
follow
dear users of gromacs,
i updated my gromacs from 4.0.1 to 4.0.5 and now i am facing the following
problem:
using the older version of gromacs I submitted REMD jobs to our cluster (which
also was updated from suse 10.3 to suse 11.1) and two differently formatted
output files were generated: trr
> Message: 4
> Date: Tue, 1 Dec 2009 13:56:21 +
> From: Alan
> Subject: [gmx-users] Re: amber force field in Gromacs
> To: gmx-users@gromacs.org
> Message-ID:
>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Servaas,
>
> I've been following your thread. I am the developer of ac
Just a report, and sort of a fix
For parallel md runs of some large systems I get a segmentation fault when
using 8 processors (but not 4).
Using fftw 3.2.2 and openmpi 1.3.3 and gromacs 4.0.5.
I tried different versions of openmpi and fftw, but the only thing that
helped was using mpich2 ins
On Tue, December 1, 2009 at 1:54:56 AM, Neha Bharat Gajaria
wrote:
> I have downloaded topolbuild1.2.1 but cannot extract files. Can anyone help
> and check the link?
Do you mean that
gunzip topolbuild1_2_1.tgz | tar -xf -
does not work for you?
Also, please check the archives for
Hi Daniel,
The problem is likely that your vesicle is interacting with itself
over the periodic boundaries. There are regions where there is no
solvent inbetween. That means that lipids can go over from one image
to the other by diffusion, which will not be compensated by using -pbc
nojump. You se
Hi,
I've tried using trjconv -pbc nojump with a .tpr created from the first
frame of the trajectory (clustered so the vesicle should be whole). The
output trajectory starts with a complete vesicle, but small numbers of
lipid particles progressively move to places outside of the box. By the
en
Dear Servaas,
I've been following your thread. I am the developer of acpypi and
thanks for giving a try.
So, as you may already know, you are trying acpypi as amb2gmx.pl so
far, but you also seemed to have read acpypi wikis and realise that
acpypi can help you to generate the whole topology for a
hema dhevi wrote:
hai justin,
ya i am working on actual KALP tutorial only
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html
and i am using the pdb file which is given in the website. This is
the first time i am doing MD
On Tue, Dec 1, 2009 at 11:22, Henri Ervasti wrote:
> I just upgraded from Gromacs 4.0.2 to 4.0.5. I wanted to re-run some
> jobs from the previous version to see if there would be any changes in
> results. I have systems with Ryckaert-Bellemans (type 3) dihedrals and
> Fourier (type 5) dihedrals.
Dear sir,
Now I am doing a coarse graining work by using Gromacs 4.0, and I want to use
'tabulated interaction functions' for both bonded and nonbonded interation. For
bonded interactions, can I use table for improper dihedrals? I have not found
it in the mannual. Thank you.
Sincerely yours
Maybe some more info:
The mdrun ends up with following declaration:
Reading file cyclohexane_minzd.tpr, VERSION 4.0.5 (double precision)
Segmentation fault
So it seems something goes wrong either writing the .tpr file or reading
it. I also did not use double precision before with 4.0.2, but I su
Dear all,
I just upgraded from Gromacs 4.0.2 to 4.0.5. I wanted to re-run some
jobs from the previous version to see if there would be any changes in
results. I have systems with Ryckaert-Bellemans (type 3) dihedrals and
Fourier (type 5) dihedrals. The jobs with type 3 run without a problem,
but w
> --
>
> Message: 4
> Date: Tue, 01 Dec 2009 10:51:17 +0100
> From: Erik Marklund
> Subject: Re: [gmx-users] Re: amber force field in Gromacs
> To: Discussion list for GROMACS users
> Message-ID: <4b14e715.3030...@xray.bmc.uu.se>
> Content-Type: text/plain; charset=
Hi,
Vacuum simulations are trickier than in solvent, more often causing
lincs errors. Have you tried playing around with lincs order and lincs iter?
/Erik
servaas skrev:
Message: 6
Date: Tue, 01 Dec 2009 07:38:29 +1100
From: Mark Abraham
Subject: Re: [gmx-users] amber force field in Gromacs
>
> Message: 6
> Date: Tue, 01 Dec 2009 07:38:29 +1100
> From: Mark Abraham
> Subject: Re: [gmx-users] amber force field in Gromacs
> To: Discussion list for GROMACS users
> Message-ID: <4b142d45.5050...@anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> servaas wrot
> Date: Tue, 1 Dec 2009 07:44:51 +1100
> From: mark.abra...@anu.edu.au
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Tabulated potentials make newbies crazy
>
> ms wrote:
> > Mark Abraham ha scritto:
> > > Sorry, I was a bit incomplete last night. Charge groups are the
> >> fundamenta
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