>
> 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 v
Lemkul, thanks
At 2011-05-25 18:56:59，"Justin A. Lemkul" wrote:
>
>
>牛继南 wrote:
>> Hi，gmx users:
>> Recently, I have a question——what's the philosophy of -ci option in
>> "genbox"?
>> My understanding is that a molecule is randomly generated in the hole at
>> first, then a new location around th
HI GMX-users,
I am trying to run a REMD simulation on my system. I have created 10 .tpr
files and fired the simulation using the following command
-
bsub -n 40 -o out_1 -e err_1 mpirun mdrun_d -s MD.tpr -multi 10 -replex 2 -o
MD.trr -e MD.edr -g MD.log -c MD.gro &
-
20 is hydrogen atom.
Sorry its typing mistake.
Nilesh
On Fri, May 27, 2011 3:52 am, Vitaly Chaban 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 paste
vivek sharma wrote:
HI GMX-users,
I am trying to run a REMD simulation on my system. I have created 10
.tpr files and fired the simulation using the following command
-
bsub -n 40 -o out_1 -e err_1 mpirun mdrun_d -s MD.tpr -multi 10 -replex
2 -o MD.trr -e MD.edr -g MD.lo
It does not change the situation, I believe.
What is the sense of calculating such ACF? In order to understand the
cross-correlation between the bonded atoms? It will be huge as I
understand.
--
Dr. Vitaly V. Chaban, Department of Chemistry
University of Rochester, Rochester, New York 14627-021
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
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
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
As I said before, g_velacc treats all the atoms in your index file as
if they were identical. It does NOT subtract anything.
On Fri, May 27, 2011 at 8:19 AM, Nilesh Dhumal wrote:
> I am calculating OH stretching frequency by fourier transform of velocity
> autocorrelation function.
>
> I coul
How can I calculate the velocity autocorrelation function of a bond with
Gromacs?
Nilesh
On Fri, May 27, 2011 8:32 am, Vitaly Chaban wrote:
> As I said before, g_velacc treats all the atoms in your index file as
> if they were identical. It does NOT subtract anything.
>
>
>
>
> On Fri, May 27,
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 14.39, 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
Hi,
I have recently done two simulations on a protein at high temperature near its
melting temperature. At the beginning I used CHARMM forcefield, and then OPLSAA
to double check the results. There are some differences in the structures
between the forcefield used. I know different forcefields
simon sham wrote:
Hi,
I have recently done two simulations on a protein at high temperature
near its melting temperature. At the beginning I used CHARMM forcefield,
and then OPLSAA to double check the results. There are some differences
in the structures between the forcefield used. I know
On 2011-05-27 17.50, simon sham wrote:
Hi,
I have recently done two simulations on a protein at high temperature
near its melting temperature. At the beginning I used CHARMM forcefield,
and then OPLSAA to double check the results. There are some differences
in the structures between the forcefiel
On 2011-05-27 10:50:14AM -0500, simon sham wrote:
> Hi,
> I have recently done two simulations on a protein at high temperature near
> its melting temperature. At the beginning I used CHARMM forcefield, and then
> OPLSAA to double check the results. There are some differences in the
> structures
Friends,
I am a newbie to gromacs, trying to calculate the Schlitters entropy
calculation using the following commands.
g_covar -f mytraj.xtc -s structure.pdb -n index.ndx -b 0 -e 4000 -mwa
-ref
g_anaeig -entropy -temp 300
When i used the above commands, i get the Schlitter entropy value for
On 2011-05-27 18.11, Bala subramanian wrote:
Friends,
I am a newbie to gromacs, trying to calculate the Schlitters entropy
calculation using the following commands.
g_covar -f mytraj.xtc -s structure.pdb -n index.ndx -b 0 -e 4000 -mwa
-ref
g_anaeig -entropy -temp 300
The formula contains ma
Hi,
Once again, I appreciate all the responses.
1. To correct I just had in the previous email. I used GROMOS53ab not CHARMM.
My apology.
2. At high temperaure, one of the helical turn in a alpha helix (3 residues)
turns into a coil in GROMOS forcefield throughout the 20ns simulation. It was
onl
Dear users,
I want to investigate *Ligand effect *on the protein .
To investigation the interaction of protein-ligand:
*RMSD calculations:*
1.
a) RMSD of Backbone
b) RMSD of Backbone+ligand
2.
a) RMSD of Protein
b) RMSD of Protein+ligand
3.
a) RMSD of Protein-H
b) RMSD of Protein-H+ligand
Which on
Hi,
I have two questions about using g-helix and g_rotacf
On g_helix,
1. I have used the following command:
"g_helix -s md.tpr -f md.xtc -n index.ndx -b 1 -e 2"
In the index file, I have residues 10-20 as my group.
However, when I ran the above command, I did not have the n-ahx.
On 28/05/2011 2:05 AM, Peter C. Lai wrote:
On 2011-05-27 10:50:14AM -0500, simon sham wrote:
Hi,
I have recently done two simulations on a protein at high temperature near its
melting temperature. At the beginning I used CHARMM forcefield, and then OPLSAA
to double check the results. There are
Hi,
I just want to say thank you to everyone who took the time to respond to my
post about the VACF of water. I really, really appreciate it.
I made a very silly mistake: I equilibrated the system for 5 ns... only to
throw it all away! It was a very big mistake on my part, and without your
he
Quoting simon sham :
Hi,
Once again, I appreciate all the responses.
1. To correct I just had in the previous email. I used GROMOS53ab
not CHARMM. My apology.
2. At high temperaure, one of the helical turn in a alpha helix (3
residues) turns into a coil in GROMOS forcefield throughout the 20
Quoting ahmet y?ld?r?m :
Dear users,
I want to investigate *Ligand effect *on the protein .
To investigation the interaction of protein-ligand:
*RMSD calculations:*
1.
a) RMSD of Backbone
b) RMSD of Backbone+ligand
2.
a) RMSD of Protein
b) RMSD of Protein+ligand
3.
a) RMSD of Protein-H
b) RMSD
Please do not send unsolicited private requests for help. The gmx-users
mailing list is appropriate. I am forwarding there without the file
attachments.
You should not mix force fields
http://www.gromacs.org/Documentation/How-tos/Parameterization
Your actual errors suggest you do not have in
Hi
I want to get the rotational axis about the protein domain motion.
*From the DynDom website => "DynDom* is a program to determine domains,
hinge axes and hinge bending residues in proteins where two conformations
are available."
Questions:
1. Do the hinge axes represent the rotational axis abou
Dear users,
I ran a simulation of a protein in water with rlist = rcoloumb = 1.4nm,
rvdw = 1.0nm, with PME and the distance between in the periodic
was set to a minimum of 2.0 i.,e distance between protein and cell
edge was set to 1.0nm, Even then, when I ran g_mindist, there was
a message stating
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