On 4/3/13 11:13 AM, Oleksandr Sushko wrote:
Dear Gromacs users,
can you help me please with next issue:
I'm analysing solvation shell of water molecules around a protein.
I use g_select to select different layers of water based on distance criteria.
The output index file contains all the atoms
300.00 K
> and corresponding refactor 1.0 / 3.0*V*k_B*T*EPSILON_0: 7.120911
> Too less points for a fit.
>
> I am not sure, where to find the dipole moment for each of the four molecules.
>
> Many thanks
> Andreas
>
>
> > -Original Message-
> >
.@gromacs.org]
> On Behalf Of Dommert Florian
> Sent: 04 August 2011 12:31
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] g_dipoles - averaging
>
> On Thu, 2011-08-04 at 09:08 +0100, Kukol, Andreas wrote:
> > Hello,
> >
> > Is there any
On Thu, 2011-08-04 at 09:08 +0100, Kukol, Andreas wrote:
> Hello,
>
> Is there any way to output the dipole moment averaged over all molecules or
> for each molecule separately (and not the total dipole moment of the
> simulation box) ?
>
Yes, the tool g_current decomposes the total dipole m
Nilesh Dhumal wrote:
Hello,
I have a system with a glucose molecule.
I want to calculate the dipole moment of a particular OH in glucose
molecule.I made an index file which have a group containing atoms.
[ O8 ]
8 18
10 is oxygen no. and 20 is hydroen no.
I'm assuming you mean 8 is O
Dear Emanuel,
Please, check
http://lists.gromacs.org/pipermail/gmx-users/2010-March/049316.html
and Berk reply.
I did never use -av (-a ?) option, maybe there is similar bug in average.xvg.
Anyway last column of Mtot.xvg gives really correct norm of M_tot vector!
Regards,
Dmitri
-
On 2010-06-04 09.45, Emanuel Peter wrote:
Dear Gromacs users,
I have following question which regards to the g_dipoles tool.
In order to get information about the total dipole moment of my protein I wrote
following command:
g_dipoles -f *.trr -s *.tpr -n *.ndx -o Mtot.xvg -a average.xvg
When
e of a charged
> molecule.
>
> Berk
>
> --
> Date: Tue, 17 Mar 2009 10:44:47 -0400
> Subject: Re: [gmx-users] g_dipoles
> From: rams.c...@gmail.com
> To: gmx-users@gromacs.org
>
>
> Dear David,
>
> The peptide is having a -ve charge of 3. Though the compon
s are possible for the dipole of a charged molecule.
Berk
Date: Tue, 17 Mar 2009 10:44:47 -0400
Subject: Re: [gmx-users] g_dipoles
From: rams.c...@gmail.com
To: gmx-users@gromacs.org
Dear David,
The peptide is having a -ve charge of 3. Though the components might dependent
upon the orientation bu
Dear David,
The peptide is having a -ve charge of 3. Though the components might
dependent upon the orientation but the average might be the same
irrespective of the orientation I suppose.
Ram.
On Tue, Mar 17, 2009 at 3:54 AM, David van der Spoel
wrote:
> rams rams wrote:
>
>> Dear Users,
>>
>>
rams rams wrote:
Dear Users,
I am trying to obtain the dipole moment of a 40 amino acid residue
peptide using g_dipoles. I am getting a huge number (about 700 Debye). I
expect it to be around 150 Debye (based on other studies). To make sure
it I extracted a shapshot of the structure and obtai
4, 2008 6:01:38 PM
Subject: Re: [gmx-users] g_dipoles questions
Semen Esilevsky wrote:
Dear David,
Thank you for reply! However there are still some question:
Dear All,
I have few questions about g_dipoles, which are not explained in the manual:
1) What method is used to calculate the epsi
Semen Esilevsky wrote:
Dear David,
Thank you for reply! However there are still some question:
Dear All,
I have few questions about g_dipoles, which are not explained in the manual:
1) What method is used to calculate the epsilon? Is there a reference which can
be cited? Is it suitable for w
Dear David,
Thank you for reply! However there are still some question:
>> Dear All,
>> I have few questions about g_dipoles, which are not explained in the manual:
>> 1) What method is used to calculate the epsilon? Is there a reference which
>> can be cited? Is it suitable for water solutions
Semen Esilevsky wrote:
Dear All,
I have few questions about g_dipoles, which are not explained in the manual:
1) What method is used to calculate the epsilon? Is there a reference
which can be cited? Is it suitable for water solutions?
In principle it is suitable for solutions of neutral molecul
Martin Höfling wrote:
Hi Folks,
I struggle with the output of g_dipoles, just to make sure that I understood
it right:
I select a subpart of my simulation and get the following output:
Average volume over run is 216
Dipole moment (Debye)
-
Average = 0.4463 Std. Dev.
Guido Humpert wrote:
Hello again,
Thanks for your responses and suggestions.
I think I understood the way epsilon is calculated in the source code,
although I'm not very fermiliar with C.
My question now is about your best bet of simulating the peptides in
different concentration of water.
What
Hello again,
Thanks for your responses and suggestions.
I think I understood the way epsilon is calculated in the source code,
although I'm not very fermiliar with C.
My question now is about your best bet of simulating the peptides in
different concentration of water.
What kind of simulation woul
Guido Humpert wrote:
Hello,
I want to use g_dipoles to calculate the dielectric constant epsilon of
peptides. The peptides contain between 20 and 40 Aminoacids and are
solvated in dodecahedron water box.
How can I define the -mu option in a system with a water solvated
peptid?
your problem is
On Tue, 2006-08-01 at 12:39 +0200, Guido Humpert wrote:
> Hello,
>
> I want to use g_dipoles to calculate the dielectric constant epsilon of
> peptides. The peptides contain between 20 and 40 Aminoacids and are
> solvated in dodecahedron water box.
> How can I define the -mu option in a system wit
+++ Bob Johnson [Wed, May 24, 2006 at 08:37:01PM -0400]:
> for some reason and I can't interepret it. The first column is the position of
> the water slab. I can only assume that column 2 is the dipole in the x
> direction and column 3 is the dipole in the y direction and so on. Is that
> correct?
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