Dear All,
Do you know how can I calculate angular distribution of all angles in my
system? Shall I specify in one index group all e.g. 80 atoms so g_angle
will calculate all possibile distributions and plot it as a sum?
Steven
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Hello all,
I was trying to calculate the normal-normal angle between the two six
membered rings using g_sgangle. I was considering the 3 atoms to
define the plane for each six membered ring but I am not getting the
correct values of normal-normal angle from g_sgangle in this way.
Please suggest me
On 26/07/2012 4:12 AM, Broadbent, Richard wrote:
Virtual sites are by definition have no mass.
If you simply ignore the mass of the carbon the molecule will be too light
and its translational momentum will therefore be too small meaning it will
move too quickly.
If you place half the mass of th
Virtual sites are by definition have no mass.
If you simply ignore the mass of the carbon the molecule will be too light
and its translational momentum will therefore be too small meaning it will
move too quickly.
If you place half the mass of the carbon on each oxygen the moment of
inertia will
Ok, read the topic about the acetonitril. But i'm somewhat clueless:
Why is the following setup wrong:
Use 2 particles as normal atoms. Put the third as a dummy in between.
Give each particle its 'normal' mass?
I would assume that this system should have the right mass and moment of
inertia, du
Sorry I should mention it at the very beginning that I have a linear
molecule and the angle is to be constrained at 180 degree. So what is
the best way of constraining the angle for the linear molecule ?
On Tue, Jul 24, 2012 at 2:06 PM, Mark Abraham wrote:
> On 24/07/2012 6:07 PM, Broadbent, Ric
On 24/07/2012 6:07 PM, Broadbent, Richard wrote:
An Angle constraint amounts to fixing a triangle. To do this you need to
constrain the distances between all the atoms as you know the of the bonds
6064, 6063 and 6063, 6065 and the angle between the two bonds it is a
trivial geometry problem calcu
An Angle constraint amounts to fixing a triangle. To do this you need to
constrain the distances between all the atoms as you know the of the bonds
6064, 6063 and 6063, 6065 and the angle between the two bonds it is a
trivial geometry problem calculate the length of the third side of the
triangle (
Oh ! Thnaks
I saw that table, the angle_restrain option is there but not constraints .
Anyway if suppose, I fix the distance between the two terminal atoms
of the molecule, the angle will eventually be fixed at a particular
given value. Is that the logic ?
Actually I searched for this problem so ma
On 24/07/2012 3:21 PM, tarak karmakar wrote:
Dear All,
I am constraining one angle in my protein sample by incorporating " [
constraints ]" block in topology file as
[ constraints ]
; index1 index2 index3 funct angle
6064 6063 6065 1 180.0
while doing that its showing the fo
Dear All,
I am constraining one angle in my protein sample by incorporating " [
constraints ]" block in topology file as
[ constraints ]
; index1 index2 index3 funct angle
6064 6063 6065 1 180.0
while doing that its showing the following error
Program grompp, VERSION 4.5.5
Sou
Hi all
I'm trying to simulate a UTP (Uridin Tryphosphate) with charge -4:
O(-) O(-) O(-)
| | |
--O--P--O--P--O--P--O(-)
| | |
O O O
I've used the triphosphate charge parameters published by Oliveira et
al(1). They used the RESP procedure after ca
Hi,
have look to the orient package for vmd:
http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/orient/
In the vmd script repository there is also a python script:
http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/fit_angle/
I have done a script using orient which calculate th
There must be several tools to calculate the angle between two domains
connected at a hinge. I was wondering if someone has suggestions on any
tools, or whether it is possible to do this using a vmd plugin directly for
a trajectory? IN my case, I have a reasonable good idea where the hinge is.
I wa
There's at least one problem that I see:
dt = 0.0001 ! just to see if it starts
This line won't be parsed properly. Check your mdout.mdp to see what grompp is
assigning as a value for dt. You shouldn't need to set a value this small to
see if it's going to work or
The mdp file is attached.
Best,
Gyorgy
Quoting "Justin A. Lemkul" :
gyorgy.han...@fc.up.pt wrote:
Dear all,
I am setting up a simulation of ionic liquids with the PF6 anion.
According to the potential, the anion should be kept rigid, wich
obviously means that bond lengths and angles
gyorgy.han...@fc.up.pt wrote:
Dear all,
I am setting up a simulation of ionic liquids with the PF6 anion.
According to the potential, the anion should be kept rigid, wich
obviously means that bond lengths and angles have to be constrained.
LINCS doesn't work with angle constraints (i.e. co
Dear all,
I am setting up a simulation of ionic liquids with the PF6 anion.
According to the potential, the anion should be kept rigid, wich
obviously means that bond lengths and angles have to be constrained.
LINCS doesn't work with angle constraints (i.e. constraing a
triangle), so we
- Original Message -
From: subarna thakur
Date: Thursday, June 10, 2010 16:41
Subject: [gmx-users] angle restraints
To: gmx-users@gromacs.org
---
|
> hello > I want to add angle restraints in my itp file for a ligand. w
hello
I want to add angle restraints in my itp file for a ligand. what is the proper
way of inserting angle restraint in .itp file ? Is there any keywords I have to
add to my .mdp file for angle restraints? I have searched the mail archieve,
I found many things about adding dihedral angle restra
You could load your gro and trr file into vmd, label the angle, save the
file and plot using excel.
Oly
On 28 April 2010 22:26, Justin A. Lemkul wrote:
>
>
> Nilesh Dhumal wrote:
>
>> Hello,
>> I am doing solvation of glucose. I am trying to calculate a angle between
>> three selected carbon at
Nilesh Dhumal wrote:
Hello,
I am doing solvation of glucose. I am trying to calculate a angle between
three selected carbon atoms.
If I run g_angle using angle.ndx file it consider all carbon atom. In
force field C-C-C 112.5 is specified so it’s making a group of all carbon
atoms. I am interest
Hello,
I am doing solvation of glucose. I am trying to calculate a angle between
three selected carbon atoms.
If I run g_angle using angle.ndx file it consider all carbon atom. In
force field C-C-C 112.5 is specified so its making a group of all carbon
atoms. I am interested in selected carbon ato
On 1/11/10 9:05 PM, Krzysztof Mlynarczyk wrote:
I'm not sure if this can be done with any of the gromacs tools, but
using the linalg module from numpy library will help you. But be aware
that a flip by 180 degrees is meaningful for you, but
undistinguishable for the mathematical procedure. This i
I'm not sure if this can be done with any of the gromacs tools, but
using the linalg module from numpy library will help you. But be aware
that a flip by 180 degrees is meaningful for you, but
undistinguishable for the mathematical procedure. This issue can be
more or less easily solved depending o
Dear gmx-users,
I have a molecule with two rings and would like to
calculate the angle between the normal vector of these rings.
Anyone have idea of how this can be done?
eef
__
Eudes Eterno Fileti
Centro de Ciências Naturais e Humanas
Universidade Federal do ABC
According to the manual "With g_rdf it is also possible to calculate an
angle dependent rdf g_{AB}(r, \theta)".
But I could not find any such specific option from "g_rdf -h". Has it been
actually implemented yet?
Regards,
Suman.
___
gmx-users mailing l
Dear gmxusers
I want to calculate the angle between 2 alpha helix. One of the
possibility to do, is g_bundle command. If I want to use g_bundle I have a
problem to define the groups in the index file. On a basis of which
criteria could I choose the 3 group in index file as input for g_bundle???
B
Morteza Khabiri wrote:
Dear gmxusers
I want to calculate the angle between 2 alpha helix. One of the
possibility to do, is g_bundle command. If I want to use g_bundle I have a
problem to define the groups in the index file. On a basis of which
criteria could I choose the 3 group in index file as
Dear gmxusers
I want to calculate the angle between 2 alpha helix. One of the
possibility to do, is g_bundle command. If I want to use g_bundle I have a
problem to define the groups in the index file. On a basis of which
criteria could I choose the 3 group in index file as input for g_bundle???
B
I am getting a warning from grompp about an angle restraint I have
specified:
WARNING 1 [file test1.top, line 18]
Duplicate atom index (1211) in angle_restraints
I specified the angle the same way as in gromacs 3.3, and I have seen no
documentation suggesting that angle restraints are spe
ED]>
To: Discussion list for GROMACS users
Date: Tue, 06 May 2008 15:03:30 +0200
Subject: Re: [gmx-users] Angle definition in g_hbond ...
sharada wrote:
>
> Hi,
>
> Thank you all for the response, Yes, the backbone of my protien does
> not have the required -Hydrogens for the
, 5 May 2008 23:13:25 +0530
Subject: Re: [gmx-users] Angle definition in g_hbond ...
Hi,
Just calculate the no. of atoms according to the choice of options and
manually. you will understand why is it giving the error. Secondly check
how gromacs calculate the no. of hydrogen bonds. It uses the c
;[EMAIL PROTECTED]>
To: "Discussion list for GROMACS users"
Date: Mon, 5 May 2008 23:13:25 +0530
Subject: Re: [gmx-users] Angle definition in g_hbond ...
Hi,
Just calculate the no. of atoms according to the choice of options and
manually. you will understand why is it giving the error
Hi,
Just calculate the no. of atoms according to the choice of options and
manually. you will understand why is it giving the error. Secondly check
how gromacs calculate the no. of hydrogen bonds. It uses the cut-off 0.35 nm
and 30 in version 3.3.1, but in earlier version the angle cut-off was 60
Mark Abraham wrote:
sharada wrote:
dear gmx-users,
I have a very fundamental query. I am trying to obtain the backbone
hydrogen bonds formed during a 15ns simulation of a 35 long protein.
When I do this by using g_hbond and selecting the Backbone groups, I
am getting no hydrogen bonds at all
sharada wrote:
dear gmx-users,
I have a very fundamental query. I am trying to obtain the backbone
hydrogen bonds formed during a 15ns simulation of a 35 long protein.
When I do this by using g_hbond and selecting the Backbone groups, I am
getting no hydrogen bonds at all . However, when I pl
dear gmx-users,
I have a very fundamental query. I am trying to obtain the backbone hydrogen
bonds formed during a 15ns simulation of a 35 long protein. When I do this by
using g_hbond and selecting the Backbone groups, I am getting no hydrogen bonds
at all . However, when I plot the hydrogen bo
you mah try to use VMD progam for trajectory analysis. In this program, you can
visuluaze the change of bond angle through the simulation.
Zuzana Benkova <[EMAIL PROTECTED]> schrieb:
Dear GMX users,
I want to analyse th ebond angle. I have used
mk_angndx -s md1.tpr -n angle.ndx
to prep
Dear GMX users,
I want to analyse th ebond angle. I have used
mk_angndx -s md1.tpr -n angle.ndx
to prepare an index for g_angle.
After
g_angle -f md1.xtc -s md1.tpr -n angle.ndx
I have obtained
Software inconsistency error:
Not supported in get_stx_coordnum
Most likely this is a trivial que
Try g_angle -h
more specific g_angle -ov
Alok
- Original Message -
From: "SWAPNA" <[EMAIL PROTECTED]>
To: "Discussion list for GROMACS users"
Sent: Monday, February 18, 2008 4:48 PM
Subject: [gmx-users] angle and dihedral as a function of time
Hi,
Is ther
Hi,
Is there a way to calculate angle & dihedral angle as a function of time?
I have tried using g_angle & g_dih. They calculate angle distribution
but not angle as a function of time.
Thanks!!
Swapna
--
The logic of life lies exclusively neither in the most incredible
detail, nor in the most s
n list for GROMACS users
Sent: Monday, October 29, 2007 10:37:13 AM
Subject: Re: [gmx-users] angle between helices
HI David
there are options like g_helix, g_angle and as you said g_bundle, but none of
them gives the angle between helix pairs.
anupam
> Marc F. Lensink wrote:
>> On Mon,
From: "Anupam Nath Jha" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To: "Discussion list for GROMACS users"
Subject: Re: [gmx-users] angle between helices
Date: Mon, 29 Oct 2007 16:07:13 +0530 (IST)
HI David
there are options like g_heli
HI David
there are options like g_helix, g_angle and as you said g_bundle, but none of
them gives the angle between helix pairs.
anupam
> Marc F. Lensink wrote:
>> On Mon, Oct 29, 2007 at 05:31:18PM +1100, Mark Abraham wrote:
>>> Anupam Nath Jha wrote:
Dear all
can i calculate the angl
On Mon, Oct 29, 2007 at 09:54:08AM +0100, David van der Spoel wrote:
> Marc F. Lensink wrote:
> >On Mon, Oct 29, 2007 at 05:31:18PM +1100, Mark Abraham wrote:
> >>Anupam Nath Jha wrote:
> >>>Dear all
> >>>can i calculate the angle between trans-membrane alpha-helices by using
> >>>gromacs?
> >>Pro
Marc F. Lensink wrote:
On Mon, Oct 29, 2007 at 05:31:18PM +1100, Mark Abraham wrote:
Anupam Nath Jha wrote:
Dear all
can i calculate the angle between trans-membrane alpha-helices by using
gromacs?
Probably. Check out section 7.4 of the manual.
i wrote a program for that. contact me off-li
On Mon, Oct 29, 2007 at 05:31:18PM +1100, Mark Abraham wrote:
> Anupam Nath Jha wrote:
> >Dear all
> >can i calculate the angle between trans-membrane alpha-helices by using
> >gromacs?
>
> Probably. Check out section 7.4 of the manual.
i wrote a program for that. contact me off-list.
as soon
Anupam Nath Jha wrote:
Dear all
can i calculate the angle between trans-membrane alpha-helices by using gromacs?
Probably. Check out section 7.4 of the manual.
Mark
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Dear all
can i calculate the angle between trans-membrane alpha-helices by using gromacs?
thanks
anupam
--
Science is facts; just as houses are made of stone, so is science is made of
facts; but a pile of stones is not a house, and a collection of facts is not
necessarily science.
Anupam Nat
Hi,
If you convert the unit to kcal/mol you'll find that both potentials
are likely coarse approximations - roughly 120 degrees equilibrium
angle, and roughly 70kcal/mol for the force constant.
Cheers,
Erik
On Jun 16, 2007, at 6:55 AM, Mark Abraham wrote:
Hi,
While performing simu
> Hi,
> While performing simulations of urea in water using the AMBER port
> for GROMACS, I noticed that the harmonic angle potential parameters in
> AMBER99 port (in ffamber99bon.itp) for the angle HNH
> (hydrogen-nitrogen-hydrogen) are (120,292.88), which are exactly the
> same parameters us
Hi,
While performing simulations of urea in water using the AMBER port
for GROMACS, I noticed that the harmonic angle potential parameters in
AMBER99 port (in ffamber99bon.itp) for the angle HNH
(hydrogen-nitrogen-hydrogen) are (120,292.88), which are exactly the
same parameters used by GR
All,
Page 160-161 of the GROMACS 3.3 manual discusses how it is possible to
use g_rdf to calculate an angle-dependent radial distribution
function. However, neither the in-manual documentation for g_rdf, nor
g_rdf -h, explains how this angle-dependent option can be used (i.e.,
how does one specif
Maarten,
What version of the code are you using? There was a bug in the angle
restraints code until 3.3.1 (or 3.3 cvs) which caused angle restraints
to turn off gradually as a function of lambda in free energy
calculations, if I remember correctly. (See bugzilla for details:
http://bugzilla.groma
Dear users,
I have a small system with a number of small peptides. I want to
constraint the angle between the N-term to C-term vectors of different
peptides. This works well, but if I do a FEP calculation the dG/dl
becomes smaller than zero at some point.
I expected it to be at least allways grea
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