Dear GROMACS-ians,
I have created an infinite graphene sheet and upon running grompp, I get
the following response:
/Warning: 1-4 interaction between 10085 and 10445 at distance 19.679
which is larger than the 1-4 table size 1.000 nm
Warning: 1-4 interaction between 9244 and 9963 at distance
Dear Mark,
When I set the option -vdwd up to a higher value, that problem is solved. So
the error message is lost. Thanks a lot for your reply.
Sincerely,
Chaofu Wu
On 09/21/09, xiao shijun xshi...@gmail.com wrote:
Mark wrote:
xiao shijun wrote:
Hi everyone,
Recently, I met a problem on the force-field. I am doing something
on the calcium carbonate, and want to simulation it with gromacs.
The shell model for oxygen has been
Darrell Koskinen wrote:
Dear GROMACS-ians,
I have created an infinite graphene sheet and upon running grompp, I get
the following response:
/Warning: 1-4 interaction between 10085 and 10445 at distance 19.679
which is larger than the 1-4 table size 1.000 nm
Warning: 1-4 interaction between
Dear Mark,
I passed your suggestion to omit the -s flag to the person who developed the
scripts to launch GROMACS on the grid (I'm only a final user with no
permission to modify the scripts). We made several trials and I don't know
exactly all the modifications he applied during all trials (it's
You should also be aware that when you determine a PDF for a distance
constrained in 3D, you will always get a trivial entropy contribution
of -2 kT log(r), which will eventually make all curves tend downwards.
Berk
Date: Sun, 20 Sep 2009 20:28:02 -0400
From: jalem...@vt.edu
To:
Date: Mon, 21 Sep 2009 09:11:24 +0200
From: anna.marabo...@isa.cnr.it
To: gmx-users@gromacs.org
Subject: [gmx-users] Re: Re: problems running REMD on grids
Dear Mark,
I passed your suggestion to omit the -s flag to the person who developed the
scripts to launch GROMACS on the grid
I assume that atoms from opposite ends of the simulation box are being seen
by GROMACS as being 1-4 neighbors as a result of the PBC,
Are you sure? have you looked at the last good frame before this message?
GMX treats PBC as it should during MD neighbour search, so maybe this is a
pair that
There were no groups specified in the neutralize.mdp file. I specified the
solvent and DNA and it worked.
Thanks.
On Sun, Sep 20, 2009 at 2:32 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Gunnar Widtfeldt Reginsson wrote:
Hi. I am new to Gromacs and I am following the tutorial on
Hi,
Is anyone who can clear the "Walls" feature in the gmx 4.0.x? Same as
Yves (see the end), I cannot find any related reference or publication
citing it.
Generally the potential on wall is in continuum format. But if it is
also true here, what the "wall_density" for? I guess it is
Hi,
Nearly all the information is in the mdp options page, but it is a bit concise.
The only really missing information is that there is not cut-off for the wall.
All atoms feel the force of one or both walls.
The density is required to determine the interaction strength of the wall
for the 9-3
Dear Gromacs users,
I am trying to run a urea+protein simulation and encountering a few problems
at various stages.
I have taken an equilibrated 10M urea box of size 2.84nmx2.84nmx2.84nm (I
started with 3x3x3 containing 160 urea + 398 SOL, ran NPT @ 1 bar and 300K)
I am using this equilibrated
Stefan Hoorman wrote:
The distances between the two structures in each of the windows
are (in nm):
0ps = 1.56 ; 500ps = 1.54; 1000ps = 1.56; 1500 = 1.56; 2000 =
1.52; 2500
= 1.65; 3000 = 1.66; 3500 = 1.77; 4000 = 1.63; 4500 = 1.62; 5000
= 1.7;
5250 = 1.62;
karan syal wrote:
Dear Gromacs users,
I am trying to run a urea+protein simulation and encountering a few
problems at various stages.
I have taken an equilibrated 10M urea box of size 2.84nmx2.84nmx2.84nm
(I started with 3x3x3 containing 160 urea + 398 SOL, ran NPT @ 1 bar and
300K)
I
Hello, everyone,
Do anybody knows how to calculate the scalar correlation matrix
across the alpha carbon atoms, where the correlation function is defined as:
Cij=delta_ri*delta_rj/squart(delta_ri^2delta_rj^2).
Is there any direct command can do this in gromacs? Thanks.
*
*
Hey,
after some pain of merging the dev branch into our 4.0.5 version I got
the new pull mode direction_periodic
running over the weekend. There's some weird rotation of the pulled
objects going on and pbc seem weird as well (there are water molecules
in those positions where I'd expect the
I tested on your system and got good results.
There is still a tricky issue: the pull COM is still determined
in the standard way by summing distances from the pbcatom.
Therefore atoms should not change nearest image from he pbcatom.
This would result in nasty noise in the pull COM and force.
I
With master branch you mean the code I get via
|git clone git://git.gromacs.org/gromacs.git
right?
Alex
|
Berk Hess schrieb:
I tested on your system and got good results.
There is still a tricky issue: the pull COM is still determined
in the standard way by summing distances from the
Yes.
Berk
Date: Mon, 21 Sep 2009 14:42:43 +0200
From: alexander.h...@mytum.de
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] direction_periodic
With master branch you mean the code I get via
|git clone git://git.gromacs.org/gromacs.git
right?
Alex
|
Berk Hess
Hi,
Check out the modified g_covar version with correlations, which is on
the user contributions.
Ran.
sheerychen wrote:
Hello, everyone,
Do anybody knows how to calculate the scalar correlation
matrix across the alpha carbon atoms, where the correlation function
is defined as:
Hi There,
I use Mac OSX 10.6.1 kernel 64 bits with Fink 64 bits.
I have a long $PATH, with several paths for several applications. If I
try 'grompp', is gives:
grompp
:-) G R O M A C S (-:
[1]33088 abort grompp
It also happens if running SLeopard
Hi,
I guess the problem is in src/gmxlib/futil.c,
where several string buffers that contain the path are of size 512.
In Gromacs 4.1 they will be 4096.
You can try replacing all numbers 512 by 4096 in src/gmxlib/futil.c.
Berk
From: alanwil...@gmail.com
Date: Mon, 21 Sep 2009 13:59:54 +0100
HI Berk,
Thanks for your reply!
Questions related the implicit Walls.
a) When I use PBC =xyz in combination with nwall=2, I get the following
error
ERROR: walls only work with pbc=xy
But If I use pbc=xy, there is no periodic image in the Z
direction, why should we use
Hi,
For all interactions except for the PME mesh part there is no pbc in z.
For PME mesh there is periodicity in z.
For c) there are several options.
One issue is that the DD setup is not very smart (yet)
and it might decompose is z. If this is case, use the -dd option
of mdrun to preferable
Stefan Hoorman wrote:
The distances between the two structures in each of the windows
are (in nm):
0ps = 1.56 ; 500ps = 1.54; 1000ps = 1.56; 1500 = 1.56; 2000 =
1.52; 2500
= 1.65; 3000 = 1.66; 3500 = 1.77; 4000 = 1.63; 4500 = 1.62; 5000
= 1.7;
Thanks Berk, although I didn't test it yet, it makes sense.
Many thanks.
Alan
On Mon, Sep 21, 2009 at 14:10, gmx-users-requ...@gromacs.org wrote:
Hi,
I guess the problem is in src/gmxlib/futil.c,
where several string buffers that contain the path are of size 512.
In Gromacs 4.1 they will
Hey,
ok, I checked this. It works ok with the assembly kernels on my local
machine, but it fails with fortran kernels
on the HPC and on my local machine.
Alex
Berk Hess schrieb:
Yes.
Berk
Date: Mon, 21 Sep 2009 14:42:43 +0200
From: alexander.h...@mytum.de
To: gmx-users@gromacs.org
Stefan Hoorman wrote:
I have a test set which is comprised of the same constituents of my real
system, except the solvent (i mean, it is in vacuum. This test set I use
to (as the name says) test different different parameters without having
to wait too much. I know it would not serve as a
Hi,
Don't use fortran.
We will get rid of it before the 4.1 release.
Berk
Date: Mon, 21 Sep 2009 16:17:17 +0200
From: alexander.h...@mytum.de
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] direction_periodic
Hey,
ok, I checked this. It works ok with the assembly kernels on my
Dear Justin,
Thanks for the reply!
I will surely try minimize the protein in Vacuum and then try adding Urea
again.
Just that i was wondering how will that effect my artifact bonds which are
between Urea and Water, and not at all between any Protein atom and
Urea/Sol?? As i mentioned earlier,
karan syal wrote:
Dear Justin,
Thanks for the reply!
I will surely try minimize the protein in Vacuum and then try adding
Urea again.
Just that i was wondering how will that effect my artifact bonds which
are between Urea and Water, and not at all between any Protein atom and
Urea/Sol??
Indeed. The key bit of information not explicitly stated in 8.5, but
present in g_analyze -h, is that normalization is on by default. The
correlation function is only dimensionless if it has been normalized
(subtract mean from all data points, divide by standard deviation). A
normalized
karan syal wrote:
Dear Justin,
Thanks for the reply!
I will surely try minimize the protein in Vacuum and then try adding
Urea again.
Just that i was wondering how will that effect my artifact bonds which
are between Urea and Water, and not at all between any Protein atom and
Urea/Sol??
2009/9/21 gmx-users-requ...@gromacs.org
Send gmx-users mailing list submissions to
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Stefan Hoorman wrote:
I have a test set which is comprised of the same constituents of my real
system, except the
Mark,
Thank you for the reply.
However it is not the definition of the autocorrelation function, isn't it?
Autocorrelation function C(t) is generally normalized by C(0), and
eq.(8.9) in the manual can be used to calculate C(t). (please
correct me if I'm wrong)
As I mentioned in my original post,
Stefan Hoorman wrote:
I am starting again my calculations for the real system and this am
going to use as starting positions distances in intervals of 0.1nm. Some
of them aren't really 0.1nm apart since the distance between the
twogroups in my first trajectory does not always increase in a
Hello together,
i refer here to the problem with msd mentioned at the beginning of
September (see also below): i calculate msd this time for monomers
(not for molecules as before) and i still observe finite size effects
for chains if they include fixed bonds ([constrains]), however this
I host a podcast with Jeff Squyres (of OpenMPI), and we would like to
have a gromacs dev on our show.
If this is something you would like to do please email me. The
interview takes about an hour and is done remotely.
Thank you!
Brock Palen
www.umich.edu/~brockp
Center for Advanced
Brock Palen wrote:
I host a podcast with Jeff Squyres (of OpenMPI), and we would like to
have a gromacs dev on our show.
If this is something you would like to do please email me. The
interview takes about an hour and is done remotely.
When?
Thank you!
Brock Palen
www.umich.edu/~brockp
On Sep 21, 2009, at 3:03 PM, David van der Spoel wrote:
Brock Palen wrote:
I host a podcast with Jeff Squyres (of OpenMPI), and we would like
to have a gromacs dev on our show.
If this is something you would like to do please email me. The
interview takes about an hour and is done
You were right Justin. I had to include the lines:
#ifdef _FF_AMBER
[ moleculetype ]
; molname nrexcl
Na+1
[ atoms ]
; idat type res nr residu name at name cg nr charge
mass
1 amber99_31 1 Na+ Na 1 1
Stefan Hoorman wrote:
I am starting again my calculations for the real system and this am
going to use as starting positions distances in intervals of 0.1nm. Some
of them aren't really 0.1nm apart since the distance between the
twogroups in my first trajectory does not always increase
Stefan Hoorman wrote:
Stefan Hoorman wrote:
I am starting again my calculations for the real system and this am
going to use as starting positions distances in intervals of
0.1nm. Some
of them aren't really 0.1nm apart since the distance between the
twogroups
Hi every body.
i would like to know if is possible to obtain a gr for only and atom of a
molecule to other atom, that is, not the mass center of the molecule.
for your help thanks
___
gmx-users mailing listgmx-users@gromacs.org
Hi Omer,
The atoms in question are part of a graphene sheet and are located at
two opposite ends of the box. They should not move as they are bound
inside the graphene sheet. The initial separation between these atoms is
19.678 nm, which is the same distance as in the warning message. So the
Hi Mark,
I did not have the statement periodic_molecules = yes in the .mdp
files. I only had the statement pbc=xyz in the .mdp files.
So, I added the periodic_molecules = yes statement to the .mdp files
and ran the simulation again. However, this did not appear to resolve
the problem as I
Darrell Koskinen wrote:
Hi Mark,
I did not have the statement periodic_molecules = yes in the .mdp
files. I only had the statement pbc=xyz in the .mdp files.
So, I added the periodic_molecules = yes statement to the .mdp files
and ran the simulation again. However, this did not appear to
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