On Thu, Jul 4, 2013 at 5:38 AM, Ishwor wrote:
> Dear all
> I have calculated the diffusion coefficient using command g_msd and I want
> to calculate diffusion coefficient using command g_velacc. I am confused
> with some terms.
> 1>I have looked the manual page of g_velacc and i found the stateme
On 2013-07-04 05:38, Ishwor wrote:
Dear all
I have calculated the diffusion coefficient using command g_msd and I want
to calculate diffusion coefficient using command g_velacc. I am confused
with some terms.
1>I have looked the manual page of g_velacc and i found the statement "the
time interva
Dear all
I have calculated the diffusion coefficient using command g_msd and I want
to calculate diffusion coefficient using command g_velacc. I am confused
with some terms.
1>I have looked the manual page of g_velacc and i found the statement "the
time interval between data collection points is
Hello,
I am calculating the velocity auto-correlation function for my system
which have 128 cation and 128 anion.
How the program calculate the total velocity auto-correlation function?
Does it average the velocity over all atoms at each time step?
Thanks
Nilesh
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Nilesh Dhumal wrote:
Hello,
I am calculating the velocity autocorrelation function for my
system. I have to calculate the g_velacc for 5 different groups within
system. I have made the index file.
I have also written .sh script
g_velacc -f 6.trr -s 6.tpr -n glu-emi-dmp-128-no.ndx -nonormal
Hello,
I am calculating the velocity autocorrelation function for my
system. I have to calculate the g_velacc for 5 different groups within
system. I have made the index file.
I have also written .sh script
g_velacc -f 6.trr -s 6.tpr -n glu-emi-dmp-128-no.ndx -nonormalize -o
h20-vac.xvg
24
g_
Hello,
I am trying to calculate the velocity autocorrelation function for my
system. I have a system with glucose + ionic liquids (128 emi (cations)
and 128 Cl (anions)).
I am not getting proper velocity autocorrelation function.
g_velacc -f 6.trr -s 6.tpr -n glu-emi-cl-128-no.ndx -nonormalize
Hello,
I am trying to calcualte the velocity autocorrelation function for my
system. I have a system with glucose + ionic liquids (128 emi (cations)
and 128 Cl (anions)).
I am not geting proper velocity autocorrelation function.
g_velacc -f 6.trr -s 6.tpr -n glu-emi-cl-128-no.ndx -nonormalize
Hello,
I am trying to calcualte the velocity autocorrelation function for my
system. I have a system with glucose + ionic liquids (128 emi (cations)
and 128 Cl (anions)).
I am not geting proper velocity autocorrelation function.
g_velacc -f 6.trr -s 6.tpr -n glu-emi-cl-128-no.ndx -nonormalize
On 2011-05-27 14.39, Nilesh Dhumal wrote:
How can I calculate the velocity autocorrelation function of a bond with
Gromacs?
READ OUR ANSWERS.
Nilesh
On Fri, May 27, 2011 8:31 am, David van der Spoel wrote:
On 2011-05-27 14.26, Nilesh Dhumal wrote:
I am calculating OH stretching frequen
How can I calculate the velocity autocorrelation function of a bond with
Gromacs?
Nilesh
On Fri, May 27, 2011 8:31 am, David van der Spoel wrote:
> On 2011-05-27 14.26, Nilesh Dhumal wrote:
>
>> I am calculating OH stretching frequency by fourier transform of
>> velocity autocorrelation functi
On 2011-05-27 14.26, Nilesh Dhumal wrote:
I am calculating OH stretching frequency by fourier transform of velocity
autocorrelation function.
I could calculate the OH stretching frequnecy by calculating fourier
transform of OH bond.
I want to know how gromacs calculate the velocity autocorrela
Nilesh Dhumal wrote:
I am calculating OH stretching frequency by fourier transform of velocity
autocorrelation function.
I could calculate the OH stretching frequnecy by calculating fourier
transform of OH bond.
I want to know how gromacs calculate the velocity autocorrelation function
of a
I am calculating OH stretching frequency by fourier transform of velocity
autocorrelation function.
I could calculate the OH stretching frequnecy by calculating fourier
transform of OH bond.
I want to know how gromacs calculate the velocity autocorrelation function
of a bond (If I define a bond
On 2011-05-26 22.48, Nilesh Dhumal wrote:
Hello,
I have calculated the velocity autocorrelation function of OH bond
in glucose molecule. For this calculation I modified the index file. The
modified part is pasted below.
[ O10 ]
10 20
where is the hydrogen?
g_velacc knows nothing about bo
Hello,
I have calculated the velocity autocorrelation function of OH bond
in glucose molecule. For this calculation I modified the index file. The
modified part is pasted below.
[ O10 ]
10 20
10 is oxygen no. and 20 is oxygen.
I used following command to calculate the velocity autocorrelati
Hello,
I am trying to calculate the velocity autocorrelation function of OH bond
in glucose molecule.
The calculate velocity autocorrelation function is not smooth. Its
fluctuating a lot so I am geting wide/think line.
Why I am not geting a smooth line?
I am using gromacs version 4.0.7.
Thanks
On 2011-04-20 18.30, Luis Martins wrote:
I'm a recent gromacs user and right now I'm starting to calculate
velocity autocorrelation functions for a pure compound, using g_velacc.
I'd like to know something more about the properties and consequences of
the option -mol and what exactly the program
I'm a recent gromacs user and right now I'm starting to calculate velocity
autocorrelation functions for a pure compound, using g_velacc.
I'd like to know something more about the properties and consequences of the
option -mol and what exactly the program does if the option is not included.
I'm
Dear Users,
I am trying the calculate the velocity autocorrelation function of
molecules. g_velacc has the -mol option.
I would like to know/confirm how the velocity autocorrelation function of
*molecules* is calculated. Is it calculated from the center of mass velocity
of each of the molecules?
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On 02/01/2011 05:49 PM, Nilesh Dhumal wrote:
> Hello,
>
>
> I am trying to calculate the Velocity Autocorrelation Function for my
> system using g_velacc. I have system of 128 ionic liquids (128 cations and
> 128 anions). I run the trajectory for 20
Hello,
I am trying to calculate the Velocity Autocorrelation Function for my
system using g_velacc. I have system of 128 ionic liquids (128 cations and
128 anions). I run the trajectory for 20 ns. I used following command
.
g_velacc -f 3.trr -n emi-etso4-127-no.ndx -s 3.tpr -o
I selected "syst
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On 10/14/2010 01:33 PM, Eudes Fileti wrote:
> Hi Florian, in fact I had already realized that it was possible
> to calculate the VACF without using the -m option (although this option
> was important for my calculations).
>
> I have not received any
Hi Florian, in fact I had already realized that it was possible
to calculate the VACF without using the -m option (although this option
was important for my calculations).
I have not received any attachment, have you send me something?
If necessary, please, send it to my email.
Following your sug
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On 10/12/2010 11:12 PM, Eudes Fileti wrote:
> Hi everybody, I'm trying to use g_velacc to calculate the diffusion
> coeficient for my solute.
> For this, I performed a simple simulation to test such tool.
>
> 1000 water molecules,
> NPT ensemb
Hi everybody, I'm trying to use g_velacc to calculate the diffusion
coeficient for my solute.
For this, I performed a simple simulation to test such tool.
1000 water molecules,
NPT ensemble
positions and velocities colected every 0.01ps
Gromacs 4.5.
However, once I run: g_velacc -f traj -s
Hi all,
I am trying to do velocity auto-correlation function(VACF) for the
'oxygen atom' present in a 63 Ang. cubic water box, simulated upto 500ps.
And the velocities are stored at every 5fs. While doing the
analysis(g_velacc), it got struck at 400ps, since if felt it is mainly due
to the mem
rams rams wrote:
Dear Users,
I am trying to calculate the velocity correlation functions to estimate
the diffusion constant of my protein which is having nearly 50 residues.
I am using the following command:
g_velacc -f .trr -s .tpr -n .ndx -o .xvg -fitfn exp
the output is the following:
C
Dear Users,
I am trying to calculate the velocity correlation functions to estimate the
diffusion constant of my protein which is having nearly 50 residues. I am
using the following command:
g_velacc -f .trr -s .tpr -n .ndx -o .xvg -fitfn exp
the output is the following:
COR:
COR: Correlation t
2008/8/5 David van der Spoel <[EMAIL PROTECTED]>:
> Vitaly Chaban wrote:
>>
>> Hi,
>>
>> I calculate the diffusion constants via Green-Kubo relation for a
>> system of 216 molecules (5 sites in each). The velocities are saved
>> every 0.005 ps and the total trajectory is 1000 ps long. Then applying
Vitaly Chaban wrote:
Hi,
I calculate the diffusion constants via Green-Kubo relation for a
system of 216 molecules (5 sites in each). The velocities are saved
every 0.005 ps and the total trajectory is 1000 ps long. Then applying
g_velacc -nonormalize -mol -n index.ndx -acflen 1001
The process s
Hi,
I calculate the diffusion constants via Green-Kubo relation for a
system of 216 molecules (5 sites in each). The velocities are saved
every 0.005 ps and the total trajectory is 1000 ps long. Then applying
g_velacc -nonormalize -mol -n index.ndx -acflen 1001
The process starts and after some ti
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