thanks
Arik
Mark James Abraham wrote:
On 01/01/10, *"Justin A. Lemkul" * wrote:
Arik Cohen wrote:
>No, sorry for the confusion. The images are only from a simulation
of one protein(tmRBP_Unliganded, PDB: 2FN9). The problem seen with
BPTI was a bit different in a way that only 1 C-alpha wa
On 01/01/10, venkat wrote:I did installed fftw , not sure it is completed. while doing make command , got the following error mesage$ configure -enable-threads --enable-float--prefix=/home/pgm/fftwThis command is hopelessly garbled. Computers are literal, and so must you be when using them. Like
On 01/01/10, Asmaa Elsheshiny wrote:Dear gromacs users,I tried to make MD simulation using mdrun in the super computer by using the following script:#!/bin/sh#$ -cwd –V#$ -l h_rt=1:00:00#$ -pe mx* 4export DO_PARALLEL=”/usr/local/sge6.0/mpi/myrinet/sge_mpirun”export gromacs=/apps/gromacs/64/3
-- Forwarded message --
From: Lum Nforbi
Date: Thu, Dec 31, 2009 at 12:33 PM
Subject: What could be wrong with rdf plot?
To: gmx-users@gromacs.org
Dear all,
I am currently analyzing a system of 2000 molecules of TIP3P water on
which I performed a NPT simulation. The plot fo
On 01/01/10, "Justin A. Lemkul" wrote:Arik Cohen wrote:>No, sorry for the confusion. The images are only from a simulation of one protein(tmRBP_Unliganded, PDB: 2FN9). The problem seen with BPTI was a bit different in a way that only 1 C-alpha was "detached" (cell size ?).>If there is supposed to
On Thu, 2009-12-31 at 08:24 -0800, venkat wrote:
> I think I should be as root to do that.
Yes, you must be root to install packages (unless you use rpm switches
to redefine the root directory.)
--
--
Jussi Lehtola, FM, Tohtorikoulutettava
Again Thanks a lot
Arik
Justin A. Lemkul wrote:
Arik Cohen wrote:
No, sorry for the confusion. The images are only from a simulation of
one protein(tmRBP_Unliganded, PDB: 2FN9). The problem seen with BPTI
was a bit different in a way that only 1 C-alpha was "detached" (cell
size ?).
If
Arik Cohen wrote:
No, sorry for the confusion. The images are only from a simulation of
one protein(tmRBP_Unliganded, PDB: 2FN9). The problem seen with BPTI was
a bit different in a way that only 1 C-alpha was "detached" (cell size ?).
If there is supposed to be only a single protein in th
No, sorry for the confusion. The images are only from a simulation of
one protein(tmRBP_Unliganded, PDB: 2FN9). The problem seen with BPTI was
a bit different in a way that only 1 C-alpha was "detached" (cell size ?).
Arik
Justin A. Lemkul wrote:
Arik Cohen wrote:
Which two proteins ? I hav
Hi Nisha,
Hetero-Atom Navi is a collection of heteroatoms culled from the PDB.
http://hetpdbnavi.nagahama-i-bio.ac.jp/index.php?mode=0
However, having only one heavy-atom, ammonia is unlikely to be
usefully extracted from this resource for use in atomistic MD.
You can easily make it yourself
Arik Cohen wrote:
Which two proteins ? I have at least in beginning only one protein which
some how is divided into two along the calculation.
Any way I'll try both increasing the cell and fix it with trjconv.
Quoting your original message:
"While running a simple MD simulation with both a
It is easy to make one yourself. I would use molden to draw ammonia and save
as pdb file. You might need to minimize before using for md.
Abu
> Date: Thu, 31 Dec 2009 16:21:29 -0500
> From: nishap.pa...@utoronto.ca
> To: gmx-users@gromacs.org
> Subject: [gmx-users] pdb file for amm
Which two proteins ? I have at least in beginning only one protein which
some how is divided into two along the calculation.
Any way I'll try both increasing the cell and fix it with trjconv.
Thanks a lot
Arik
Justin A. Lemkul wrote:
Arik Cohen wrote:
I'm using dodecahedron -d 0.7
Was
nishap.pa...@utoronto.ca wrote:
Does anyone know where I can get a pdb file for ammonia? I tried
searching but I am not sure if there is a website for the pdb files I
can use in gromac. Any suggestions would be helpful.
For something simple like ammonia, you could probably just write the c
Arik Cohen wrote:
I'm using dodecahedron -d 0.7
Was that distance specified with respect to both of the protein molecules in the
unit cell? You can check for spurious PBC interactions with g_mindist -pi.
Anyway, I'd be curious to see how you do with trjconv.
-Justin
Justin A. Lemkul
I'm using dodecahedron -d 0.7
Justin A. Lemkul wrote:
Arik Cohen wrote:
Hi,
I have not tried yet to fix it with trjconv which I will . Attached
is a picture with 4 snapshots taken from the simulation. The C-alphas
in question are emphasized with red color.
Is your unit cell sufficien
Does anyone know where I can get a pdb file for ammonia? I tried
searching but I am not sure if there is a website for the pdb files I
can use in gromac. Any suggestions would be helpful.
Thanks.
Nisha
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gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listi
Arik Cohen wrote:
Hi,
I have not tried yet to fix it with trjconv which I will . Attached is a
picture with 4 snapshots taken from the simulation. The C-alphas in
question are emphasized with red color.
Is your unit cell sufficiently large? It looks like the C-alphas indicated are
simp
Arik Cohen wrote:
Hi,
Sorry to bother you again ,but its not only a periodic effect since only
*some of the atoms* in the "Detached" group are vanishing from this
group and reappearing in the main protein group. The rest of the atoms
are either always in the detached or the main group.
In
Hi,
Sorry to bother you again ,but its not only a periodic effect since only
*some of the atoms* in the "Detached" group are vanishing from this
group and reappearing in the main protein group. The rest of the atoms
are either always in the detached or the main group.
In addition, the "detach
Arik Cohen wrote:
Hi,
With regards to your question I do see some periodicity in which for a
section of time in the trajectory some of the Calphas in the "detached
group" are vanishing from it and reappear in the main protein.
In addition,
I would appreciate as before any suggestion you mig
Hi,
With regards to your question I do see some periodicity in which for a
section of time in the trajectory some of the Calphas in the "detached
group" are vanishing from it and reappear in the main protein.
In addition,
I would appreciate as before any suggestion you might have in the matter
Asmaa Elsheshiny wrote:
Dear gromacs users,
I tried to make MD simulation using mdrun in the super computer by using the
following script:
#!/bin/sh
#$ -cwd –V
#$ -l h_rt=1:00:00
#$ -pe mx* 4
export DO_PARALLEL=”/usr/local/sge6.0/mpi/myrinet/sge_mpirun”
export gromacs=/apps/gromacs/64/3.
Dear gromacs users,
I tried to make MD simulation using mdrun in the super computer by using the
following script:
#!/bin/sh
#$ -cwd –V
#$ -l h_rt=1:00:00
#$ -pe mx* 4
export DO_PARALLEL=”/usr/local/sge6.0/mpi/myrinet/sge_mpirun”
export gromacs=/apps/gromacs/64/3.3.1-ffamber20080701/bin
$ DO
ram bio wrote:
Dear Gromacs Users,
Iam following Drug/Enzyme complex solvation tutorial by John E.
Kerrigan, I am unable to execute the grompp step as per the tutorial,
the output of grompp command is as follows:
grompp -f minim.mdp -c trp_b4ion.gro -p trp.top -o trp_b4ion.tpr
I think I should be as root to do that.
- Original Message
From: Jussi Lehtola
To: Discussion list for GROMACS users
Sent: Thu, December 31, 2009 10:17:00 AM
Subject: Re: [gmx-users] gromacs 4.06 binary for linux -redhat
On Thu, 2009-12-31 at 08:09 -0800, venkat wrote:
> I did insta
On Thu, 2009-12-31 at 08:09 -0800, venkat wrote:
> I did installed fftw , not sure it is completed.
I assume you're running Red Hat Enterprise
(or any of its clones such as CentOS).
Just do things the easy way: enable Fedora EPEL
http://www.fedoraproject.org/wiki/EPEL/FAQ#howtouse
on your syste
I did installed fftw , not sure it is completed.
while doing make command , got the following error mesage
$ configure -enable-threads --enable-float--prefix=/home/pgm/fftw
$make
cp fftw_wisdom.1 fftwf-wisdom.1
make all-am
/bin/sh ../libtool --tag=CC --mode=link gcc -std=gnu99 -O3
-fomit
Dear Gromacs Users,
Iam following Drug/Enzyme complex solvation tutorial by John E.
Kerrigan, I am unable to execute the grompp step as per the tutorial,
the output of grompp command is as follows:
grompp -f minim.mdp -c trp_b4ion.gro -p trp.top -o trp_b4ion.tpr
:
Vitaly V. Chaban wrote:
Hi,
What conditions could cause the following error?
=
Fatal error:
2 particles communicated to PME node 7 are more than a cell length out
of the domain decomposition cell of their charge group
=
Please check the wiki for such things, many errors are exp
Hi,
So many posts and replies on a single issue, and still no exact
command lines, nor grompp output, nor gromacs version. Lin, please be
aware that such errors only make sense in the context of what you did.
You'll have to provide all information that might be related to it.
I'm pretty sure that
lammps lammps wrote:
Sorry for this.
Thanks for your kind reply. That is the answer of my question.
Actually, I only want to make sure whether the command of energygrp_excl
has the ability not to calculate the force in the group.
The manual about energygrp_excl seems not talk about how to d
Hi,
What conditions could cause the following error?
=
Fatal error:
2 particles communicated to PME node 7 are more than a cell length out of
the domain decomposition cell of their charge group
=
With the same system, sometimes is appears, but sometimes everything goes
smoothly (starting
Sorry for this.
Thanks for your kind reply. That is the answer of my question.
Actually, I only want to make sure whether the command of energygrp_excl has
the ability not to calculate the force in the group.
The manual about energygrp_excl seems not talk about how to deal with the
force. Maybe
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