Dear Prof.
I want to use walls (in z=0 and z=z_box) for my simulation with martini
coarse-grained force field, but always it give me error!
Do the martini force field support walls? Should I use just 12-6 for wall_type?
May I ask your help about this, Please?
Best regards
Sara--
gmx-users mai
Hi, Hernan.
You wrote 16 Jan 2012 ?., 19:23:27:
> Dear gmx-user,
> I am working in the dinamicas fo aluminophosphates material. I need to
> calculated de IR spectrum from the trajectory. if is it possible to do
> this with gromacs?,
GROMACS is great!
Couple years ago I calculated with gromacs
You can use the command genbox -cs with the option -maxsol number to
specify the number of water molecules
Good luck
Cuong
2012/1/16 vidhya sankar
> Hello Justin,
> Thanks for your patient reply
>
> I would like to solvate my molecules with specific
> number
On 17/01/2012 4:55 AM, Thomas Schlesier wrote:
Dear all,
Is there a way to omit particles with zero charge from calculations
for Coulomb-interactions or PME?
In my calculations i want to coarse-grain my solvent, but the solute
should be still represented by atoms. In doing so the
solvent-molec
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Hi all,
Has anybody used Coarse grained model for Cytochrome C? I could create a
model using MARTINI forcefiels (using martinize.py script and 1HRC.pdb
file), but it does not have HEM and HOH groups. Can anybody help me?
Kind Regards,
Dariush Mohammadyani
Department of Structural Biology
Universi
Ioannis Beis wrote:
Dear gromacs users,
I am trying to center the trajectory of a bilayer in the rectangular
simulation box in the frame of my effort to calculate the bilayer
thickness with g_dist. According to the visualization, the upper layer
of the membrane lies on the lowest part of th
Dear Gmx Users,
Can you please suggest a method (and further reading) for calculation of a
chemical potential in Gromacs. Is it possible e.g. to calculate the
chemical potential of my ligand or water in systerm consisting protein and
ligand?
Thank you
Steven
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Dear all,
Is there a way to omit particles with zero charge from calculations for
Coulomb-interactions or PME?
In my calculations i want to coarse-grain my solvent, but the solute
should be still represented by atoms. In doing so the solvent-molecules
have a zero charge. I noticed that for a si
Dear gromacs users,
I am trying to center the trajectory of a bilayer in the rectangular
simulation box in the frame of my effort to calculate the bilayer
thickness with g_dist. According to the visualization, the upper layer
of the membrane lies on the lowest part of the box and the lower
vidhya sankar wrote:
Dear Mark
Thank you for your reply.
I did As u said But when I visualize the resulting
.gro files in VMD .The solute molecules are centered (i used the center
option in editconf) But solvent molecules are are away . but within the
Dear Mark
Thank you for your reply.
I did As u said But when I visualize the resulting .gro
files in VMD .The solute molecules are centered (i used the center option in
editconf) But solvent molecules are are away . but within the box i need
Solute mole
We would like to announce the first version of a mono-objective algorithm
that use GROMACS for Protein Structure Prediction (PSP).
Although it is initial version, it was compared with other methodologies.
These results were sent to WCCI [1] congress. We would like to share them
with who are intere
I tried and it got even worse: every # of cpus configuration gave the
LINCS WARNING message.
Thanks anyway.
Alessandro
Il 16/01/2012 15.58, Dr. Vitaly V. Chaban ha scritto:
Dear users,
I would like to ask your help about understanding a problem i'm not able
to recognize by myself.
Basically, a
Thomas Schlesier wrote:
Dear all,
what is the reason, that the tabulated potential must go till r_c+1 (r_c
= cut-off radius) and not only up to r_c?
I think we only calculate the interactions till r_c and truncate the
rest. So everything behind r_c would be redundant information (due to
the
Thank for you answer. Meanwhile, our user told us that she found the
ideal configuration for running her simulations; nevertheless, i linked
her this discussion in case she can find some interesting suggestion.
Cheers,
Alessandro
Il 16/01/2012 16.05, Matthew Zwier ha scritto:
Ciao,
I've seen
Dear all,
what is the reason, that the tabulated potential must go till r_c+1 (r_c
= cut-off radius) and not only up to r_c?
I think we only calculate the interactions till r_c and truncate the
rest. So everything behind r_c would be redundant information (due to
the truncation it would be set
Ciao,
I've seen this behavior (something running fine on one core but
failing on multiple cores, or certain multiples of cores) frequently.
It's almost always due to an unstable system. Have your user try
equilibrating longer, or minimize with flexible water before trying
equilibration. You can
>
> Dear users,
> I would like to ask your help about understanding a problem i'm not able
> to recognize by myself.
> Basically, a user of our sistem (IBM SP6, power6 architecture) is trying
> to run a simulation of a very simple sistem, a polymer chain in a lot of
> water molecules. While the sim
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Dear users,
I would like to ask your help about understanding a problem i'm not able
to recognize by myself.
Basically, a user of our sistem (IBM SP6, power6 architecture) is trying
to run a simulation of a very simple sistem, a polymer chain in a lot of
water molecules. While the simulation wo
Kiwoong Kim wrote:
Hi,
I'm trying to plot the displacements in z-coordinate of each particle
belonging to some index group using g_traj.
I typed below thing in prompt
g_traj -f md_0_2_nvt.xtc -s md_0_2_nvt.tpr -n index_traj.ndx -nox -noy
-b 0 -e 50 -ox traj -w -xvg xmgrace
There are 6 a
Hi,
I'm trying to plot the displacements in z-coordinate of each particle
belonging to some index group using g_traj.
I typed below thing in prompt
g_traj -f md_0_2_nvt.xtc -s md_0_2_nvt.tpr -n index_traj.ndx -nox -noy -b 0
-e 50 -ox traj -w -xvg xmgrace
There are 6 atoms in the desired index g
Dear gmx-user,
I am working in the dinamicas fo aluminophosphates material. I need to
calculated de IR spectrum from the trajectory. if is it possible to do this
with gromacs?, if someone can help me with this (paper or reviews) it would be
great.
Best Wishes
Hernan
-
On 14/01/12 08:30, Suman Nandy wrote:
Respected Sir,
According to suggestions, in gmxusers, I have used renumtop, although it
renumbers the ligand topology, but gives a duplicate atom label.
; ERROR: duplicate atom label '4968' for atom #4968 (already used for
atom #4968)
I used the command "./
Hi everyone!
On this page
http://manual.gromacs.org/online/g_hbond.html
there is an option -r2 when using g_hbond. What is this r2? I can't find it in
the Gromacs manual. option -a is the angle H-O-O, option -r is the O-O distance
which can be switched to H-A by using the "-da no". Need help o
Thank you for your response.
I use 3.3.3 version because it's this one which is installed on the cluster,
and that is difficult to change it without causing any bug and a reviewing is
in process for the webservice. So change it now should be difficult.
To be able to select cysteins with the -ss
On 16/01/12, pitheve...@free.fr wrote:
>
> Dear all,
>
> I'm using the old 3.3.3 version of gromacs and I try to use the -ss option of
> pdb2gmx to select interactively the ss bridge in my protein.
>
> But I don't remark any change between using -ss option and not using it. The
> -inter o
Dear all,
I'm using the old 3.3.3 version of gromacs and I try to use the -ss option of
pdb2gmx to select interactively the ss bridge in my protein.
But I don't remark any change between using -ss option and not using it. The
-inter option give me some interactive options such as lys or arg but
On 16/01/12, vidhya sankar wrote:
>
>
>
>
>
>
>
>
>
>
>
>
>
> Hello Justin,
>
> Thanks for your patient reply
>
>
> I would like to solvate my molecules with specific number
> of water molecules
> what option is a su
Hello Justin,
Thanks for your patient reply
I would like to solvate my molecules with specific number of
water molecules
what option is a suitable to do that ? in editconf
with regards
S.Vidhya sankar
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