These are the actual values extracted from xpm image
Diagonal element 0.34,0.6,0.8..(which is supposed to be 1.0)
Off-diagonal elements 0.3,0.21,0.01,...(which is supposed to be zero)
Additional information.
1. Maximum force at the end of energy minimization is of the order of
2.1x10^-10 (Is it su
Success! Following your advice, and with a few tweaks everything is running
smoothly, thank you so much for your help.
all the best
Will
> Date: Thu, 3 Feb 2011 22:44:48 -0500
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Adding modified nucleotide to a force
On 4/02/2011 1:05 AM, Gordan Horvat wrote:
I'm doing molecule dynamics of a calixarene in a acetonitrile box with
pbc, energy groups defined and npT constant. When I extract
interaction energies with g_energy from edr file I expect them to be
pretty much constant because I see no significant co
william Stebbeds wrote:
Thanks again,
You were right, it was a misaligned pdb file :).
However I now get an error when I use grompp:
ERROR 1 [file newoxi.noNaCl_DNA.itp, line 1381]:
No default Bond types
ERROR 2 [file newoxi.noNaCl_DNA.itp, line 4462]:
No default Angle types
ERROR 3
Thanks again,
You were right, it was a misaligned pdb file :).
However I now get an error when I use grompp:
ERROR 1 [file newoxi.noNaCl_DNA.itp, line 1381]:
No default Bond types
ERROR 2 [file newoxi.noNaCl_DNA.itp, line 4462]:
No default Angle types
ERROR 3 [file newoxi.noNaCl_DNA.it
william Stebbeds wrote:
Thanks for the reply,
ffamber99sb.rtp entry:
[ DGO ]
[ atoms ]
Pamber99_461.16590 1
O1Pamber99_45 -0.77610 2
O2Pamber99_45 -0.77610 3
O5'amber99_44 -0.49540 4
C5'amber99_11 -0.00690 5
H5'1amber9
On 4/02/2011 12:36 PM, william Stebbeds wrote:
Thanks for the reply,
ffamber99sb.rtp entry:
[ DGO ]
[ atoms ]
Pamber99_461.16590 1
O1Pamber99_45 -0.77610 2
O2Pamber99_45 -0.77610 3
O5'amber99_44 -0.49540 4
C5'amber99_11 -0.00690
Thanks for the reply,
ffamber99sb.rtp entry:
[ DGO ]
[ atoms ]
Pamber99_461.16590 1
O1Pamber99_45 -0.77610 2
O2Pamber99_45 -0.77610 3
O5'amber99_44 -0.49540 4
C5'amber99_11 -0.00690 5
H5'1amber99_190.07540 6
H5'
On 4/02/2011 10:16 AM, Ramachandran G wrote:
Hi gmx-users,
Is there is any software available to view the vibrational modes
selectively for particular wave number from the trajectory file.
This is something that quantum chemists do a lot of, so I'm sure
GaussView and Spartan can do it. Fi
Hi gmx-users,
Is there is any software available to view the vibrational modes
selectively for particular wave number from the trajectory file.
Thanks and regards,
Rama
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Please search the ar
simon sham wrote:
Hi,
Is it possible to run simulations at high temperatures?
Just about anything is possible ;)
Is there any concern in dealing with the solvent water molecules when
running high temperature simulations?
Yes, but presumably if you have a system with a reasonable density
Hi,
Is it possible to run simulations at high temperatures?
Is there any concern in dealing with the solvent water molecules when running
high temperature simulations?
Best,
Simon Sham
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william Stebbeds wrote:
Hello,
I am attempting to add 8-oxo-dG (8-Oxo-2'-deoxyguanosine) to the
amber99sb force field. This is a simple modification of the H8 hydrogen
on a guanine to an oxygen atom. I have followed the instructions on the
gromacs site on adding residues.
However the new
Hello,
I am attempting to add 8-oxo-dG (8-Oxo-2'-deoxyguanosine) to the amber99sb
force field. This is a simple modification of the H8 hydrogen on a guanine to
an oxygen atom. I have followed the instructions on the gromacs site on adding
residues.
However the new nucleotide will not work, it w
My aim is to establish a temperature gradient in the MD simulation box. I'm
simulating a magnesium silicate system with interatomic potentials (Mg-Mg,
Mg-Si, etc.) and no bond or angle potentials.
My algorithm:
1. Divide the MD box in 12 slabs along the x-axis.
2. Pick slab 3 as my source and sla
On 2011-02-03 16.41, Kumaran Baskaran wrote:
Hi,
I am trying to understand normal mode analysis in gromacs. I just
took one amino acid(Glycine), energy minimized then calculated normal
mode eigenvectors as described in Gromacs manual(grompp,mdrun,g_nmeig).
Then I calculated the inner product
Hi,
I am trying to understand normal mode analysis in gromacs. I just
took one amino acid(Glycine), energy minimized then calculated normal
mode eigenvectors as described in Gromacs manual(grompp,mdrun,g_nmeig).
Then I calculated the inner product between them using 'g_anaeig'.
example: g_anaei
I'm doing molecule dynamics of a calixarene in a acetonitrile box with
pbc, energy groups defined and npT constant. When I extract interaction
energies with g_energy from edr file I expect them to be pretty much
constant because I see no significant conformational changes or changes
in distance
chandran karunakaran wrote:
Dear GMX-users,
I am not able to run the GMX molecular dynamics simulation of proteins
in DMSO solvent. It is not accepting the DMSO solvent and gives error. I
would be happy if
GMX users help in running for solvents other than water.
Please do not append t
Dear GMX-users,
I am not able to run the GMX molecular dynamics simulation of proteins
in DMSO solvent. It is not accepting the DMSO solvent and gives error. I would
be happy if
GMX users help in running for solvents other than water.
with thanks
***+
Dr.Karu
Dear Tusar:
Let's keep this on the mailing list.
You could learn about expr with a simple google search! It should have
worked though, did you mangle the command somehow when you typed it?
There should be " > not_last_line.gro" with a redirect at the end but
you have only a star. Neverthel
Dear Justin,
thank you very much for your always useful suggestions. I think I will use
the combination of G43a1+Berger in order to overcome the problems of using 3
different forcefields, and I will check carefully the topology created by
PRODRG for the ligand, according to your paper.
Many thanks
Thank you for your reply. I am not planning to simulate proton transfer in
gromacs. Just it could be nice to see possible interaction.
best,
Olga
2011/2/3 Erik Marklund
> Mark Abraham skrev 2011-02-03 11.59:
>
> On 3/02/2011 9:18 PM, Olga Ivchenko wrote:
>>
>>> Dear Gromacs Users,
>>>
>>> I wo
Mark Abraham skrev 2011-02-03 11.59:
On 3/02/2011 9:18 PM, Olga Ivchenko wrote:
Dear Gromacs Users,
I would like to replace some of my water molecules with H+ ions, or
add hydrogen ions to my water box. Please could you advice me how to
do it?
I'm not aware of any force field that implement
On 3/02/2011 9:18 PM, Olga Ivchenko wrote:
Dear Gromacs Users,
I would like to replace some of my water molecules with H+ ions, or
add hydrogen ions to my water box. Please could you advice me how to
do it?
I'm not aware of any force field that implements hydrogen cation
(because it is unph
Dear Gromacs Users,
I would like to replace some of my water molecules with H+ ions, or add
hydrogen ions to my water box. Please could you advice me how to do it?
Yours sincerely,
Olga
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Please
Dear Anna,
I think it's better to keep one single force field... I don't know
which ff is better for your simulation, but for example you can
manually correct the definition that PRODRG gives you and adjusting it
for GROMOS 53a6 paramenters.
Valerio
anna.marabo...@isa.cnr.it ha scritto:
Sorry, but changing the definition and using the other suggested by
Dimitris doesn't change the results, I still have the same problem in
minimisation...
Valerio
Dimitris Dellis ha scritto:
On 02/02/2011 07:47 PM, Justin A. Lemkul wrote:
Dimitris Dellis wrote:
Hi.
There is an issue w
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