Vitaly V. Chaban wrote:
Hi,
What is a correct way to include improper dihedrals into the force
field? I have four atom numbers, then dihedral value and one value of
the force constant.
[ impropers ]
1 2 3 4 2 180 N
doesn't work.
Looking through the existing force fields I did not conclude
Hi,
What is a correct way to include improper dihedrals into the force
field? I have four atom numbers, then dihedral value and one value of
the force constant.
[ impropers ]
1 2 3 4 2 180 N
doesn't work.
Looking through the existing force fields I did not conclude about an
exact syntax.
T
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 t
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
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
p
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
http://lists
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
> twogrou
>
>
> 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 alway
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
22.98977
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 remotely.
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
C
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 Computing
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
effect
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 s
>Mark,
>
>Thank you for the reply.
>
>However it is not the definition of the autocorrelation function, isn't it?
>Autocorrelation function is generally normalized by , and
>eq.(8.9) in the manual can be used to calculate . (please
>correct me if I'm wrong)
>As I mentioned in my original post, the
2009/9/21
> Send gmx-users mailing list submissions to
>gmx-users@gromacs.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
>
>
> 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
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?? As
>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 correl
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??
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, th
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
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 ve
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@gromac
Thanks Berk, although I didn't test it yet, it makes sense.
Many thanks.
Alan
On Mon, Sep 21, 2009 at 14:10, 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 be 4096.
> You can try r
>
>
> 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
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 dec
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 "wall_e
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 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 kerne
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: C
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
> |
>
>
>
> B
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
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
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 peri
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=/squart().
Is there any direct command can do this in gromacs? Thanks.
*
*
___
gmx-
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 a
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.
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 b
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
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 bas
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 wrote:
>
>
> Gunnar Widtfeldt Reginsson wrote:
>
>> Hi. I am new to Gromacs and I am following the tutorial on
>> http://wwwuser.g
> 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
>
>
> 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
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: gmx-user
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 n
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 92
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