On 10/29/13 4:02 PM, Tiago Gomes wrote:
Hello gromacs users,
I´m currently tring to calculate S2 order parameters for comparison with
nmr data and other simulations.
When i try the command for the NH vector:
g_rotacf -s ../protein.tpr -d -P 2 -n nh.ndx -f ../protein_fit.xtc -w
-noaver
It give
Hello gromacs users,
I´m currently tring to calculate S2 order parameters for comparison with
nmr data and other simulations.
When i try the command for the NH vector:
g_rotacf -s ../protein.tpr -d -P 2 -n nh.ndx -f ../protein_fit.xtc -w
-noaver
It gives me the only half of the residues (NH vecto
Hi,
I am trying to locate code for angle auto-correlation function (ACF)
in GROMACS 4.0.7. Angle ACF is calculated by g_rotacf for GROMACS
(gmx_rotacf.c). In line 194 of gmx_rotacf.c, it calls "do_autocorr".
This function is in gstat.h file line 125 - 185. But I don't see any
actual code which ca
On 4/06/2011 11:27 AM, Mark Abraham wrote:
On 4/06/2011 9:02 AM, simon sham wrote:
Hi,
I have tried to use g_rotacf to get the rotational autocorrelation
plot for a n-h vector, and I have two questions:
1. My MD run is 20ns, but the rotacf.xvg shows only 10ns. why?
This can be normal for co
On 4/06/2011 9:02 AM, simon sham wrote:
Hi,
I have tried to use g_rotacf to get the rotational autocorrelation
plot for a n-h vector, and I have two questions:
1. My MD run is 20ns, but the rotacf.xvg shows only 10ns. why?
This can be normal for computed correlation functions. See chapter 5.
Hi,
I have tried to use g_rotacf to get the rotational autocorrelation plot for a
n-h vector, and I have two questions:
1. My MD run is 20ns, but the rotacf.xvg shows only 10ns. why?
2. The plot is bottom out at 500 ps and then go back up. What does it mean
physically?
Thanks for your insight.
Dear gromacs users,
I want to calculate NH vector for my ligand simulations using g_rotacf. I
want to ask if I first need to remove rotation and translation degrees of
freedom from the trajectory using the command:
trjconv -f traj.xtc -s 10nsProd_MD.tpr -fit rot+trans -o no_rot_trans.xtc
Also, wh
henri mone wrote:
Der Gromacs users and dear Justin,
The gromacs tutorial does not really tell how to create a "tpr"
without a "mdp" file. The standard procedure in the tutorials is to
use the program "grompp" which always requires a "mdp" file. But for
calculating the autocorrelation function
Der Gromacs users and dear Justin,
The gromacs tutorial does not really tell how to create a "tpr"
without a "mdp" file. The standard procedure in the tutorials is to
use the program "grompp" which always requires a "mdp" file. But for
calculating the autocorrelation function I only need the coord
henri mone wrote:
Dear Gromacs experts and newbies,
The program "g_rotacf" (calculates the autocorrelation function)
requires as input for the -s option either a "tpr", "tpb" or "tpa"
file.
I does not accept for the -s option a PDB file :- ( .
How can I create from a "pdb" file a "tpr" file?
T
Dear Gromacs experts and newbies,
The program "g_rotacf" (calculates the autocorrelation function)
requires as input for the -s option either a "tpr", "tpb" or "tpa"
file.
I does not accept for the -s option a PDB file :- ( .
How can I create from a "pdb" file a "tpr" file?
The program "pdb2gmx" c
Hi,
I would say rotational acf's can be negative.
In most cases this will indicate bad sampling.
This is not suprising considering the extremely long times you printed.
I guess you get positive values for shorter correlation times.
Berk
> From: x.peri...@rug.nl
> Subject: Re:
On Sun, 11 Jan 2009 12:50:00 +0800
Dechang Li wrote:
Dear all,
I used g_rotacf to calculate the order parameter (S2, N-H bond in
main chian). Thanks to Xavier Periole's advice, I make the index file
and obtained some results. However, some results I got made me puzzling
that the order par
Dechang Li wrote:
> Dear all,
>
> I used g_rotacf to calculate the order parameter (S2, N-H bond in
> main chian). Thanks to Xavier Periole's advice, I make the index file
> and obtained some results. However, some results I got made me puzzling
> that the order parameter is negative! Here
Dear all,
I used g_rotacf to calculate the order parameter (S2, N-H bond in
main chian). Thanks to Xavier Periole's advice, I make the index file
and obtained some results. However, some results I got made me puzzling
that the order parameter is negative! Here is one of my results:
@t
Daniel K wrote:
How should I change it so it calculates the 40 ps?
You need at least a 80ps trajectory otherwise you basically have too
less data to correlate with with a lag time of 40ps.
Check gromacs manual 4.0 at section 8.5
On Wed, Oct 22, 2008 at 6:34 PM, Xavier Periole <[EMAIL PROTECTE
How should I change it so it calculates the 40 ps?
On Wed, Oct 22, 2008 at 6:34 PM, Xavier Periole <[EMAIL PROTECTED]> wrote:
> On Wed, 22 Oct 2008 17:38:58 -0400
> "Daniel K" <[EMAIL PROTECTED]> wrote:
>
>> I have been trying to use g_rotacf with a simulation run for 40 ps (2)
>> with steps
On Wed, 22 Oct 2008 17:38:58 -0400
"Daniel K" <[EMAIL PROTECTED]> wrote:
I have been trying to use g_rotacf with a simulation run for 40 ps (2)
with steps of 2fs and the frames where extracted every 50 fs (25 frames).
The trajectory file is correct because it has 801 frames. When I calculate
I have been trying to use g_rotacf with a simulation run for 40 ps (2)
with steps of 2fs and the frames where extracted every 50 fs (25 frames).
The trajectory file is correct because it has 801 frames. When I calculate
the g_rotacf I only get 20 ps and the time step is 50 fs. Does any body no
Dear users,
The default -normalize option in g_rotacf is set to yes. Does it mean that
the vector of interest is always be a unit vector ?
If so, this has to be set to -nonormalize I suppose if one is interested
about the internal dynamics of a system. Please let me know whether I am
correct or
Dear Xavier,
Thank you very much for your valuable inputs. I am extremely sorry for
troubling you quite often.
You are absolutely right and I am using the second order legendre
polynomials to obtain the correlation function only (am not using this to
fit the correlation function data). The correl
One thing I totally forgot to mention is that you can not access the
overall rotational motion of the protein using the NH vectors!
These would contain both internal and overall motion.
Have a look at papers from Lipari and Szabo JACS-1982 for the initial model
and from Bruschweiler Current Opin
On Thu, 4 Sep 2008 21:13:39 -0400
"rams rams" <[EMAIL PROTECTED]> wrote:
Hi Xavier,
I have a question about the accuracy of the correlation times obtained using
gromacs tools. (I am getting these by integrating the output .xvg file of
g_rotacf using g_analyze). Since the experimental values are
Hi Xavier,
I have a question about the accuracy of the correlation times obtained using
gromacs tools. (I am getting these by integrating the output .xvg file of
g_rotacf using g_analyze). Since the experimental values are not available
to compare, I am not so sure about the correlation times I am
On Thu, 4 Sep 2008 09:45:34 -0400
"rams rams" <[EMAIL PROTECTED]> wrote:
Hi Xavier,
I am extremely sorry for incomplete information. But this is a follow up to
my previous two emails. Unfortunately I havent received any suggestions for
them and it appears like you too missed them. For more clar
Hi Xavier,
I am extremely sorry for incomplete information. But this is a follow up to
my previous two emails. Unfortunately I havent received any suggestions for
them and it appears like you too missed them. For more clarity I am pasting
them here again:
Dear users,
To calculate the rotationa
On Wed, 3 Sep 2008 23:40:14 -0400
"rams rams" <[EMAIL PROTECTED]> wrote:
Hi,
I am so surprised for not finding any one who have better experience with
g_rotacf. I have been playing around with it and the time correlation value
I got by g_rotacf is so small in comparison to the time correlation
Hi,
I am so surprised for not finding any one who have better experience with
g_rotacf. I have been playing around with it and the time correlation value
I got by g_rotacf is so small in comparison to the time correlation value I
calcualted using the hydrodynamic radius of the protein. The value i
Dear users,
I have given a command like the following to calculate the rotational auto
correlation function:
g_rotacf -f .trr -s .tpr -P 2 -fft -o .xvg -b -e 1 -n .ndx -d
I want to use the second order Legendre polynomial to fit. I integrated the
resulting .xvg file, to obtain the cor
Dear users,
To calculate the rotational auto correlation functions, the command
mentioned in the maual is:
g_rotacf -P 1 -nparm 2 -fft -n index -o .xvg -fa -beginfit -endfit
what are the -nparm and -fa options are meant for ?
Also do we need to use -fitfn option to obtain the rotational auto
c
Hi,
I am sorry if it is the second time I am posting the same thing. Two days
back I have posted this but myself couldnt get a copy of the mail. So I am
not very sure whether it reached the others member or not.
I want to clarify a few of the things about the usage of g_rotacf (for
rotational cor
Hi,
I want to clarify a few of the things about the usage of g_rotacf (for
rotational correlation function for molecules). In the manual it is given
like the following:
g_rotacf -P 1 -nparm 2 -fft -n index -o rotacf-x-P1 -fa expfit-x-P1
-beginfit 2.5 -endfit 20.0
I understood that -f, -s options
Rama Gullapalli wrote:
Dear All
I have what might be a simple question. For g_rotacf, what is the
equation used in the calculation of the rotational correlation function?
is there any basic reference one could give me for the same?
Also, for the rotational correlation function, is the decay som
Dear All
I have what might be a simple question. For g_rotacf, what is the equation used
in the calculation of the rotational correlation function? is there any basic
reference one could give me for the same?
Also, for the rotational correlation function, is the decay something as simple
as the
Hi Rama,
You would be able to do it by taking one of two approaches:
1. Write the centers of masses and from this generate a multipdb file
(or gro file) containing three atoms spanning two vectors
perpendicular to the vector between these centers of masses. This
trajectory can be used for g_rota
Hello everybody.I have question regarding g_rotacfIf I wanted to compute the rotational correlation function of a linear vector which is between the "centers of masses" of two groups of atoms in an individual molecule (Instead of two atoms), how do I go about it?Can I use g_rotacf to do it ?Thanks
Dear Dr Spoel Sorry for the earlier hasty mail. I figured out how the -noaver option works. Thanks Sincerely Regards RamaRama Gullapalli <[EMAIL PROTECTED]> wrote: Dear Dr SpoelThank you for the reply. But I do not quite follow how -noaver does it. I want to compute the P-N vector of lipid mo
Dear Dr SpoelThank you for the reply. But I do not quite follow how -noaver does it. I want to compute the P-N vector of lipid molecules and average it over the 128 molecules in the bilayer.Do I make a group containing the numbers of the P and N molecules in a single group ( 256 atoms) and use g_r
On Fri, 22 Sep 2006, Rama Gullapalli wrote:
>Hello everybody,
>
> I have nearly 100 different vectors to analyse using g_rotacf. I was
> wondering if there was anyway to do this in GROMACS simultaneously since
> g_rotacf does not have have the -ng option like in g_traj or others.
>
-noa
Hello everybody,I have nearly 100 different vectors to analyse using g_rotacf. I was wondering if there was anyway to do this in GROMACS simultaneously since g_rotacf does not have have the -ng option like in g_traj or others.I would imagine one could use a awk script to run g_rotacf to
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