Ramachandran G wrote:
Thank you for the reference. But still i like check it out for my
system. But still i don't know how to get 'S' type hydrogen bonding.
I am pasting my screen output below:
You need to pass the -life option.
--
Dears,
I would like to know if the details of how to add new post-processing
features in Gromacs had been already discussed or described somewhere.
I have in mind things like angle distribution, structure factor, and
incoherent intermediate scattering function, to name a few, for glassy
materials.
Thanks allot for all your help
Arik
Mark Abraham wrote:
Arik Cohen wrote:
Dear users,
Is there a way(in the mdp file) to take a snapshot of only the
C-alpha atoms along a trajectory if certain condition are met(tested
every time a snapshot needs to be taken) ?
If you know in advance you'l
Arik Cohen wrote:
Dear users,
Is there a way(in the mdp file) to take a snapshot of only the C-alpha
atoms along a trajectory if certain condition are met(tested every time
a snapshot needs to be taken) ?
If you know in advance you'll only ever want the C-alpha atoms for
analysis (dangerous
Santan William wrote:
Hey all,
I wanted to install gromacs on one node of a cluster. Firstly I
downloaded all needed packages to /home/william/software, then unpack
all of them under this folder.
Then, I followed the " Quick and Dirty Installation" instruction
using following
Hey all,
I wanted to install gromacs on one node of a cluster. Firstly I
downloaded all needed packages to /home/william/software, then unpack all of
them under this folder.
Then, I followed the " Quick and Dirty Installation" instruction
using following commands:
export SOFT=$HOME
> Dear All,
>
> when I want to use grompp program
> grompp -f minim.mdp -c solboxbrady.gro -p bradymod.top -o
> minimbrady.tpr
>
> I got the following error message
>
> Fatal error:
> [ file "spc.itp", line 41 ]:
> Atom index (1) in settles out of bounds (1-0)
>
> So I tried to m
Thanks for all your help and rapid response.
Arik
Justin A. Lemkul wrote:
Arik Cohen wrote:
Dear users,
Is there a way(in the mdp file) to take a snapshot of only the
C-alpha atoms along a trajectory if certain condition are met(tested
every time a snapshot needs to be taken) ?
No, bu
Arik Cohen wrote:
Dear users,
Is there a way(in the mdp file) to take a snapshot of only the C-alpha
atoms along a trajectory if certain condition are met(tested every time
a snapshot needs to be taken) ?
No, but you could probably script it after the trajectory is run, using whatever
a
Dear users,
Is there a way(in the mdp file) to take a snapshot of only the C-alpha
atoms along a trajectory if certain condition are met(tested every time
a snapshot needs to be taken) ?
Thanks
Arik
___
gmx-users mailing listgmx-users@gromacs.o
Thank you for the reference. But still i like check it out for my
system. But still i don't know how to get 'S' type hydrogen bonding.
I am pasting my screen output below:
-
abelius wrote:
Dear All,
I would like to work on the R61 DD-peptidase enzyme complexed with
penicillin G and cephalosporin C. The antibiotics are covalently bound
and up till now I used gromacs/oplsaa for simulations on the apo enzyme
but I'm struggling with the FF parametrization of the
Dear All,
I would like to work on the R61 DD-peptidase enzyme complexed with
penicillin G and cephalosporin C. The antibiotics are covalently bound
and up till now I used gromacs/oplsaa for simulations on the apo enzyme
but I'm struggling with the FF parametrization of the antibiotics.
Ca
Englebienne, P. wrote:
Hi all,
I’m looking to perform simulations on a series of synthetic co-polymers
containing a variety of building blocks. I will be testing different
sequences of the monomers, therefore I am looking for a way to
streamline the generation of the topologies.
I hav
wuxiao wrote:
> Dear GMXers,
> I want to calculate the inter- and intra-molecular radial distribution
> functions (rdfs), separately. However, I find the g_rdf routine can only
> be useful to calculate the total rdf. Is there any similar routine which
> can be used to reach my aim? Please give
Hi Abhijit,
I think the Zinc ion goes with chain B and uses the same identifier.
Given the fact that you didn't quite understand the error, and found
it necessary to post a question, this raises another question: should
you be wanting to simulate a protein with a zinc ion?
(http://www.gromacs.org/
abhijit kayal wrote:
Hello everyone
I am going to analysis the PDB file 3GJN.pdb.After giving the pdb2gmx
it shows the fatal error
"chain identifier 'B' was used in two non-sequential blocks (residue
404, atom 3227)".So what is the solution for this.
The error message i
Hello everyoneI am going to analysis the PDB file 3GJN.pdb.After giving the
pdb2gmx it shows the fatal error
"chain identifier 'B' was used in two non-sequential blocks (residue 404,
atom 3227)".So what is the solution for this.
Thank you
Abhijit
__
Hi!
I never used TMD, but this homepage (and the mail address on it) might
help you:
http://markt.bph.rub.de/~juergen/
Greets,
Christian.
Am Freitag, den 02.10.2009, 11:52 +0530 schrieb sanja...@iitb.ac.in:
> I want to simulate a comformation change of a protein from state A to B.
> >Fr
ram bio wrote:
Dear Justin,
As suggested, when i reexamined the system.gro (protein_newbox +
dppc128) one of the ends of the problem (as i think) i.e. few
aminoacids of protein were beyond the water surface of the bilayer,
probably this may be the reason for the presence of water molecules to
There is no need to post three times in five minutes. If someone has advice,
they will attend to your post in due time.
This issue is commonly reported. Making haphazard changes to your topology is a
bad idea. Please search the list archive (available through the interface at
the Gromacs
Hi Pablo,
I would write .rtp entries and so on for each monomer.
You copy the modified files into your working directory.
Have a great day,
Andrea
2009/10/6 Englebienne, P.
> Hi all,
>
>
>
> I’m looking to perform simulations on a series of synthetic co-polymers
> containing a variety of bui
Dear Justin,
As suggested, when i reexamined the system.gro (protein_newbox +
dppc128) one of the ends of the problem (as i think) i.e. few
aminoacids of protein were beyond the water surface of the bilayer,
probably this may be the reason for the presence of water molecules to
the side of the bil
Dear All,
when I want to use grompp program
grompp -f minim.mdp -c solboxbrady.gro -p bradymod.top -o minimbrady.tpr
I got the following error message
Fatal error:
[ file "spc.itp", line 41 ]:
Atom index (1) in settles out of bounds (1-0)
So I tried to modify the topology file b
Dear All,
when I want to use grompp program
grompp -f minim.mdp -c solboxbrady.gro -p bradymod.top -o minimbrady.tpr
I got the following error message
Fatal error:
[ file "spc.itp", line 41 ]:
Atom index (1) in settles out of bounds (1-0)
So I tried to modify the topology file b
Dear All,
when I want to use grompp program
grompp -f minim.mdp -c solboxbrady.gro -p bradymod.top -o minimbrady.tpr
I got the following error message
Fatal error:
[ file "spc.itp", line 41 ]:
Atom index (1) in settles out of bounds (1-0)
So I tried to modify the topology file b
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--
Chinmay,
I'd like to add you to my professional network on LinkedIn.
- Ajani
Accept invitation from Ajani haresh
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Hi all,
I'm looking to perform simulations on a series of synthetic co-polymers
containing a variety of building blocks. I will be testing different sequences
of the monomers, therefore I am looking for a way to streamline the generation
of the topologies.
I have been reading Chapter 5 of the
ram bio wrote:
Dear Justin,
Thanks for the advice. I am using the DPPC 128 lipid bilayer from D.
Peter Tieleman website, and the nvt.mdp file and the nvt.log files are
as follows as in your tutorial:
Constraining the starting coordinates (step 0)
Constraining the coordinates at t0-dt (st
Hi,
To get the z coordinate of the center of mass of a molecule I use the following
command:
echo "number of molecule" | g_traj -f xxx.xtc -s xxx.tpr -n xxx.ndx -nox -noy
-com -ox xxx.xvg
I guess you can create an .ndx file for a lipid head group to get the z
coordinate of this.
Regards,
Sa
Dear Justin,
Thanks for the advice. I am using the DPPC 128 lipid bilayer from D.
Peter Tieleman website, and the nvt.mdp file and the nvt.log files are
as follows as in your tutorial:
_
ram bio wrote:
Dear Gromacs Users,
I have inserted the protein in lipid bilayer and performed Inflategro
I am able to reach the required area per lipid after certain
iterations but was unable to get the standard Epot and Fmax values
that is negative and to the power of 5 or 6 and Fmax less tha
Dear Gromacs Users,
I have inserted the protein in lipid bilayer and performed Inflategro
I am able to reach the required area per lipid after certain
iterations but was unable to get the standard Epot and Fmax values
that is negative and to the power of 5 or 6 and Fmax less than 1000
during the l
Hi,
Here's my mdp file:
*+
title= Martini
integrator = md
tinit= 0.0
dt = 0.03
nsteps = 20
nstcomm = 1
nstxout = 1000
nstvout
Ramachandran G wrote:
C_HB(T) = /
S_HB(T) = /
h(T) = 1, if a pair of atoms bonded at time T,
= 0, otherwise
H(T) = 1, if a pair of atoms continously bonded
between time 0 to time T,
Hi,
You could also try g_bundle -z, it might do what you want.
Cheers
Tom
--On Tuesday, October 06, 2009 11:04:29 +0200 XAvier Periole
wrote:
g_traj with an index and playing with the different options.
On Oct 6, 2009, at 11:01 AM, Moutusi Manna wrote:
Dear all,
I want
C_HB(T) = /
S_HB(T) = /
h(T) = 1, if a pair of atoms bonded at time T,
= 0, otherwise
H(T) = 1, if a pair of atoms continously bonded
between time 0 to time T,
= 0, othe
Dear Justin,
Thanks.
Ram
On Mon, Oct 5, 2009 at 7:30 PM, Justin A. Lemkul wrote:
>
>
> ram bio wrote:
>>
>> Dear Gromacs Users,
>>
>> I am looking for a DPPC bilayer system of 256 and above , can anybody
>> suugest me the site from where I can download Please...
>>
>
> Take a pre-equilibrated 12
Ramachandran G wrote:
Dear gromacs users:
I like to know whether gromacs will calculate S-type hydrogen
bond correlation function?
If it so how it can be done? Thank you.
What does that mean?
Rama
___
gmx-users mailing listgmx-users@grom
Dear gromacs users:
I like to know whether gromacs will calculate S-type hydrogen
bond correlation function?
If it so how it can be done? Thank you.
Rama
___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo
Dear GMXers,
I want to calculate the inter- and intra-molecular radial distribution
functions (rdfs), separately. However, I find the g_rdf routine can only be
useful to calculate the total rdf. Is there any similar routine which can be
used to reach my aim? Please give me some hints. Thanks
g_traj with an index and playing with the different options.
On Oct 6, 2009, at 11:01 AM, Moutusi Manna wrote:
Dear all,
I want to calculate the vertical position (Z-axis) of
different lipid head groups as a function of time.
Looking forward for any suggestion.
Dear all,
I
want to calculate the vertical position (Z-axis) of different lipid
head groups as a function of time.
Looking forward for any suggestion.
Thanks in advance,
Moutusi Manna
Yahoo! India has a new look. Take a sneak peek http://in.yahoo.com
On Oct 5, 2009, at 16:01 , Justin A. Lemkul wrote:
/usr/lib64/gcc-lib/x86_64-suse-linux/3.3.3/../../../../x86_64-suse-
linux/bin/ld: cannot find -lX11
collect2: ld returned 1 exit status
make[3]: *** [grompp] Error 1
make[3]: Leaving directory `/CHPC/home/chpc/Test/oscar/
gromacs-4.0.5/src/ke
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