Dear all
What are the analysis tools which should be used on MD trajectory file in
order to find potential aggregation sites of a protein. Anyone can tell me
about specific resource material on use of Gromacs to predict protein
aggregation hot spots from MD trajectory anlysis.
Shahid Nayeem
--
gmx
On 12/05/2010 2:27 AM, Sai Kumar Ramadugu wrote:
Dear Gromacs Users,
I have a simulation of a protein in Truncated Octahedron box. I want
to calculate the water residence times and mean square displacements (of
water) around the active site residues. We developed our own algorithm
for doing t
Chris,
I understand, Sorry for that . Actually I mixed up the concept of SteeredMd
with umbrella sampling. So I was confused whenever you people gave
suggestions.
Now I thing I got the idea , Thanks for you people. I will try myself and
see. Thanks once again.
-Aswathy
On Tue, May 11, 2010 at
The mac computer is a cluster or just your personal computer?
If you will use it to prepare the system and for analysis you could
use macport or fink to compile gromacs.
Anthony
On Tue, May 11, 2010 at 11:13 AM, Emily Curtis
wrote:
> Dr. Bonner,
> I am trying to install gromacs on a mac. I am r
Durba Roy wrote:
Hi Gromacs Users,
I am trying to run a NVE simulation of a single dye molecule jumping
from state S0 to state S1. I have starting coordinates and velocities
from a previous NPT run of the same system at S0, however, the charges
are new, that of S1. I didnot generate any Max
Hi Gromacs Users,
I am trying to run a NVE simulation of a single dye molecule jumping
from state S0 to state S1. I have starting coordinates and velocities
from a previous NPT run of the same system at S0, however, the charges
are new, that of S1. I didnot generate any Maxwell-velocity for th
Nilesh Dhumal wrote:
Hello,
I am trying to calculate spatial distribution function (SDF) for my system.
1. trjconv -s 3.tpr -f 3.trr -o b.xtc -center -ur compact -pbc none -n
test.ndx
2. rajconv -s 3.tpr -f b.xtc -o c.xtc - fit rot+trans -n test.ndx
I am getting the following error for step
Hello,
I am trying to calculate spatial distribution function (SDF) for my system.
1. trjconv -s 3.tpr -f 3.trr -o b.xtc -center -ur compact -pbc none -n
test.ndx
2. rajconv -s 3.tpr -f b.xtc -o c.xtc - fit rot+trans -n test.ndx
I am getting the following error for step 2.
Fatal error: Index[23
Hello Justin,
Sorry. I was following the manual-4.0 for g_spatial. Maunal is giving
differnet things.
I checked with g_spartial -h. I got.
Thanks
NIlesh
On Tue, May 11, 2010 4:22 pm, Justin A. Lemkul wrote:
>
>
>
> Nilesh Dhumal wrote:
>
>> Hello Justin,
>> I am doing solvation of glucose in ion
Nilesh Dhumal wrote:
Hello Justin,
I am doing solvation of glucose in ionic liquids. I want to show that
glucose in surrounded by cation by ploting the iso-surface.
Becuase of this I am using g_sdf. THe out put file is in .plt file. Can I
get use gassview to plot the iso-surface.
I have no i
On 11/05/10 05:17, sonali dhindwal wrote:
Thanks a lot for your replies. I will start reading this and learning MD.
I really want to say that this forum is an excellent source of help.
Thanks for all your help.
Another book you may want to read is "Understanding molecular
simulation", by Daan
Hello Justin,
I am doing solvation of glucose in ionic liquids. I want to show that
glucose in surrounded by cation by ploting the iso-surface.
Becuase of this I am using g_sdf. THe out put file is in .plt file. Can I
get use gassview to plot the iso-surface.
Do you think still I can use g_spatial
Nilesh Dhumal wrote:
Hello,
I am trying to calculate spatial distribution function (SDF) for my system.
Can I genrate the *.cube file or gaussian format file using sdf?
I want to use gassview or molden software to plot.
Have you tried g_spatial -h? I think you will find what you're looking
Hello,
I am trying to calculate spatial distribution function (SDF) for my system.
Can I genrate the *.cube file or gaussian format file using sdf?
I want to use gassview or molden software to plot.
Thanks
Nilesh
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org
Dear Gromacs Users,
I have a simulation of a protein in Truncated Octahedron box. I want to
calculate the water residence times and mean square displacements (of water)
around the active site residues. We developed our own algorithm for doing
the same.
In earlier simulations I had cubic box and
On 05/11/2010 04:57 PM, XAvier Periole wrote:
On May 11, 2010, at 4:48 PM, Esteban Gabriel Vega Hissi wrote:
If we follow strictly the parameterization guides,
these are only guide lines ... no need to follow "strictly" :))
Actually this was the problem: CG seems easy because of a reduced n
Dr. Bonner,
I am trying to install gromacs on a mac. I am running Leopard. I can
configure successfully, however, when I type "make" I am getting the same
errors that you reported:
make[5]: *** [nb_kernel010_ppc_altivec.lo] Error 1
make[4]: *** [all-recursive] Error 1
make[3]: *** [all-recurs
Moeed wrote:
Dear GROMACS experts,
Initially I wanted to do MD for a stack of hexane molecules. MD showed
very high repulsion potential. On the recommendation of Justin, I
simplified the problem and now I have only one Hexane molecule.
1- I dont know why I do not get the written pdb files
Dear GROMACS experts,
Initially I wanted to do MD for a stack of hexane molecules. MD showed very
high repulsion potential. On the recommendation of Justin, I simplified the
problem and now I have only one Hexane molecule.
1- I dont know why I do not get the written pdb files normally generated
a
On May 11, 2010, at 4:48 PM, Esteban Gabriel Vega Hissi wrote:
If we follow strictly the parameterization guides,
these are only guide lines ... no need to follow "strictly" :))
Urea has to be mapped to only one CG bead (because of reduction from
4 to 1), but I believe that this would not be
If we follow strictly the parameterization guides, Urea has to be mapped to
only one CG bead (because of reduction from 4 to 1), but I believe that this
would not be able to represent properties of the molecule. Instead I would
use a 2 beads model or try something like it has been done with water,
There is no Urea topology for Martini FF. Would be very interesting to
have one!
you need to look for some properties that you be able to reproduce.
have a look at the papers!
Typically you need to find logP (partitioning data) between different
media and and reproduce it using some Martini
Hi Nahren,
You probably used make_ndx for making the index file. Unfortunately it sorts
the indices. You have to construct it in such a way that that the indices
are in the order you want them. You can script the generation, based on the
chain ID, or you can make separate index files that you conc
Dear all,
I am looking for a urea topology for some CGMD simulations performed
with the MARTINI FF.
Actually I am planning to design it on my own, but in case at least a
"source of inspiration" (I have found no papers about the issue) would
be appreciated.
Cheers,
Luca
--
Dear Tsjerk,
The trjconv is not working, it is likely that i am not issuing the proper
commands.
--- My ndx file - - -
Select group for output
Group 0 ( System) has 2619 elements
Group 1 ( Protein) has 2619 elements
Group 2 ( Protein-H) has 2619 elements
Group 3 (
It represents a difference in coordinate space. You'll get the most
out of this list if you continue to try to solve your problems before
posting and avoid submitting every question/problem that you hit upon
under a continuously in-use title. Did you try it and look at you -px
output file?
On 11/05/2010 10:45 PM, Carla Jamous wrote:
Thank you Mark,
I'm running gromacs 4.0.3., so I don't know if I should submit a bugzilla.
There's nothing in the release notes that I could see that looks like
it's been fixed.
http://www.gromacs.org/About_Gromacs/Release_Notes/Revisions_in_4.0
Thank you Mark,
I'm running gromacs 4.0.3., so I don't know if I should submit a bugzilla.
Please Do you know another way to restart my MD run?
Thanks,
Carla
On Tue, May 11, 2010 at 1:00 PM, Mark Abraham wrote:
> On 11/05/2010 7:55 PM, Carla Jamous wrote:
>
>> Hi everyone,
>>
>> please I encoun
On 11/05/2010 7:55 PM, Carla Jamous wrote:
Hi everyone,
please I encountered a problem of potential energy rising suddenly
during my simulation.
Someone advised me to take the previous conformation of my system,
center it in the box, minimize it & then restart my MD simulation, by
taking the pre
Hi everyone,
please I encountered a problem of potential energy rising suddenly during my
simulation.
Someone advised me to take the previous conformation of my system, center it
in the box, minimize it & then restart my MD simulation, by taking the
previous velocities of this conformation.
So I d
On May 11, 2010, at 11:37 AM, abdullah ahmed wrote:
Dear GROMACS users,
I have a protein structure with two oppositely charged residues
facing each other. They are close enough for an electrostatic
interaction to occur between them. However, this does not occur.
After minimization they a
Dear GROMACS users,
I have a protein structure with two oppositely charged residues facing each
other. They are close enough for an electrostatic interaction to occur between
them. However, this does not occur. After minimization they are in the exact
same positions as before.
Is there some
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