On 2010-10-18 03.30, Chih-Ying Lin wrote:
HI
I confined one molecule in the center of box and issue the g_dipole command.
The average dipole moment is still around 32.
It is the molecule with 33 atoms / united atoms of most carbon groups,
isn't the dipole moment around 32 too high?
How can I
Hello Julian.
I've not gone though the C-code neither. However, from what I have read
and understood about MSD calculation, both calculations you proposed
should not give the same results. This is the way it is calculated.
1. You take different starting times over tyour trajectory, every
At 2010-10-18 12:56:31，chris.ne...@utoronto.ca wrote:
Generally, forcefields are not parameterized for temperatures other
than 298K, so simulations are not expected to reproduce the expected
properties (like boiling water and the correct temperature
denaturation of proteins).
There's
3. Simulation parameter problem about protein unfolding (Chen)
Hi,
You write it yourself: In paper you mention, they have used a 0.8 nm
cutoff range for both electrostatics and cutoff. You are doing something
different by using PME for the electrostatics. Also you are using a much
On 2010-10-18 06.56, chris.ne...@utoronto.ca wrote:
Generally, forcefields are not parameterized for temperatures other than
298K, so simulations are not expected to reproduce the expected
properties (like boiling water and the correct temperature denaturation
of proteins).
There's almost
Hi gromacs users
I am beginner in gromacs. I did md simulation of a protein by gromacs and
now
I want to obtain residence time of water molecule and life time of hydrogen
bonds. Can I obtain both of them using gromacs?
please guide me by detail.
--
gmx-users mailing listgmx-users@gromacs.org
atila petrosian wrote:
Hi gromacs users
I am beginner in gromacs. I did md simulation of a protein by gromacs
and now
I want to obtain residence time of water molecule and life time of hydrogen
bonds. Can I obtain both of them using gromacs?
please guide me by detail.
Start by searching
Dear Justin
thanks for your attention
in my case calcium ion is bonded to 4 oxygen atoms of C=O group of protein.
yes, Calcium ions are present in nearly all the force fields in Gromacs. but
there are only parameters in * nb.itp and not in * bon.itp. how to obtain
these new parameters for my
leila karami wrote:
Dear Justin
thanks for your attention
in my case calcium ion is bonded to 4 oxygen atoms of C=O group of
protein. yes, Calcium ions are present in nearly all the force fields in
Gromacs. but there are only parameters in * nb.itp and not in * bon.itp.
how to obtain
*Dear Justin*
**
*I read manual and specially g_hbond. but manual doesn't gime me information
about * residence time of water molecule and life time of hydrogen.
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Please search the archive at
atila petrosian wrote:
*Dear Justin*
**
*I read manual and specially g_hbond. but manual doesn't gime me
information about *
residence time of water molecule and life time of hydrogen.
The more important piece of advice I gave you was to search the mailing list
archive. This same
Dear Justin
Is there any way for this problem?
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On 18/10/2010 10:15 PM, atila petrosian wrote:
*Dear Justin*
**
*I read manual and specially g_hbond. but manual doesn't gime me
information about *
residence time of water molecule and life time of hydrogen.
In your reading, did you see that g_hbond has a -life option? Did you
try
leila karami wrote:
Dear Justin
Is there any way for this problem?
Please keep Tsjerk's comments
(http://lists.gromacs.org/pipermail/gmx-users/2010-October/054938.html) in mind.
If the calcium coordination complex plays only a minor structural role, you
can probably justify using
Hi all
i added new atomtype for dichloroethane (DCE) and added the corresponding
parameters in the .rtp, .atp, .bon.itp, .nb.itp respectively. given below
are my additions to the corresponding files respectively.
*ffoplsaa.rtp*
[ DCE ]
[ atoms ]
CLAA opls_967 -0.2270 1
CAB opls_966
On 18/10/2010 10:31 PM, vinothkumar mohanakrishnan wrote:
Hi all
i added new atomtype for dichloroethane (DCE) and added the
corresponding parameters in the .rtp, .atp, .bon.itp, .nb.itp
respectively. given below are my additions to the corresponding files
respectively.
*ffoplsaa.rtp*
[
Dear Mark
I generated the topology using pdb2gmx using dce.pdb. i checked the .top
file and i contains necessary .itp files. the error message that i get is
given below. any help is highly appreciated.
Program grompp, VERSION 4.0.7
Source code file: toppush.c, line: 620
Fatal error:
Unknown
On 18/10/10 03:30, Mark Abraham wrote:
To enforce chirality in such a toy, I thought that a simple
(naive?) but functional idea could be that of enforcing a not-
too-hard and wide-bottomed dihedral restrain on the phi angle,
like that:
[ dihedral_restraints ]
; ai ajak
al type label
vinothkumar mohanakrishnan wrote:
Hi all
i added new atomtype for dichloroethane (DCE) and added the
corresponding parameters in the .rtp, .atp, .bon.itp, .nb.itp
respectively. given below are my additions to the corresponding files
respectively.
*ffoplsaa.rtp*
[ DCE ]
[ atoms ]
CLAA
On 18/10/10 03:30, Mark Abraham wrote:
To enforce chirality in such a toy, I thought that a simple
(naive?) but functional idea could be that of enforcing a not-
too-hard and wide-bottomed dihedral restrain on the phi angle,
like that:
[ dihedral_restraints ]
; ai ajak
al type label
On 18/10/10 12:49, vinothkumar mohanakrishnan wrote:
Dear Mark
I generated the topology using pdb2gmx using dce.pdb. i checked the .top
file and i contains necessary .itp files. the error message that i get is
given below. any help is highly appreciated.
What Mark meant is that you should
Please keep all Gromacs-related correspondence on the gmx-users list. As I have
said many times, I am not a private tutor. I am CC'ing this message to the
list; please continue all further discussion there.
There are a number of topology-generating scripts on the Gromacs website. Have
a
On 18/10/2010 10:53 PM, ms wrote:
On 18/10/10 03:30, Mark Abraham wrote:
To enforce chirality in such a toy, I thought that a simple
(naive?) but functional idea could be that of enforcing a not-
too-hard and wide-bottomed dihedral restrain on the phi angle,
like that:
[ dihedral_restraints ]
On 18/10/10 13:06, Mark Abraham wrote:
On 18/10/2010 10:53 PM, ms wrote:
On 18/10/10 03:30, Mark Abraham wrote:
To enforce chirality in such a toy, I thought that a simple
(naive?) but functional idea could be that of enforcing a not-
too-hard and wide-bottomed dihedral restrain on the phi
Dear Justin
what corrections i should make to ffoplsaan.itp to make it correct. what i
should give instead of CAB and CLAA?.
i copied the .rtp .atp .itp files from usr/local/gromacs/share/gromacs/top
to my working directory and added these parameters to the corresponding
files. what you mean is
On 18/10/10 13:06, Mark Abraham wrote:
On 18/10/2010 10:53 PM, ms wrote:
On 18/10/10 03:30, Mark Abraham wrote:
To enforce chirality in such a toy, I thought that a simple
(naive?) but functional idea could be that of enforcing a not-
too-hard and wide-bottomed dihedral restrain on the phi
Dear all,
when using implicit solvent models, the sa_surface_tension parameter is
set to 2.092 kJ/mol/nm2 by default.
However in Gromacs benchmarks with dihydrofolate reductase this
parameter is set to 2.25936.
Can someone please explain this parameter and in how far this would
change
vinothkumar mohanakrishnan wrote:
Dear Justin
what corrections i should make to ffoplsaan.itp to make it correct. what
i should give instead of CAB and CLAA?.
You must use atom types, not names. Unfortunately, you've chosen to use atom
names, which are also types, which makes all of
Hi!
This is unfortunately a bit confusing, but prior to the release of 4.5.2
gromacs did not use the value of
the sa_surface_tension that was specified in the mdp-file. It was always set to
2.092, and then hardcode to take a certain
value (other than 2.092) depending on the GB-model.
2.25936
At 2010-10-18 16:38:30，David van der Spoel sp...@xray.bmc.uu.se wrote:
On 2010-10-18 06.56, chris.ne...@utoronto.ca wrote:
Generally, forcefields are not parameterized for temperatures other than
298K, so simulations are not expected to reproduce the expected
properties (like boiling water
Thanks David. I think that we're saying the same thing, but there is
indeed a 'correct' denatured state at a given temperature and pressure
and protein concentration and salt concentration, etc. It was this to
which I was referring.
Chris.
On 2010-10-18 06.56, chris.neale at utoronto.ca
Chen,
to answer this, please see David's post and my reply. To answer if
your unfolded state ensemble is accurate, you will need to know some
experimentally evaluated quantities of the state that you are trying
to reproduce: 498K, 26 atm, a certain amount of salt, etc, (but not
including
Hi everyone,
I am just wondering how backups of Gromacs trajectories are handled out
there.
We are using TSM. The system is very reliable, but it does not scale well in
conjunction with Gromacs: trajectories can get very large when -append is used
(dozens of Gigabytes), but TSM cannot do
On 18/10/10 13:12, Chen wrote:
At 2010-10-18 16:38:30??David van der Spoelsp...@xray.bmc.uu.se wrote:
On 2010-10-18 06.56, chris.ne...@utoronto.ca wrote:
Generally, forcefields are not parameterized for temperatures other than
298K, so simulations are not expected to reproduce the expected
Hi,
1. For those intrinsically disordered proteins, the sequence is known, how the
simulations will be set up, I mean, the first PDB will be needed, how to get
this one? (Ideally, not necessarily to be practical)
2. suppose I got a PDB, there were several models there, let's say 16, is it
#ZHAO LINA# wrote:
Hi,
1. For those intrinsically disordered proteins, the sequence is known,
how the simulations will be set up, I mean, the first PDB will be
needed, how to get this one? (Ideally, not necessarily to be practical)
Hi,
1. Thanks for the webpage you provided, I noticed there is a avogadro there,
and right now coincidently I have a question relevant to the avogadro,
When I tried the avogadro-packmol-extensions, I had installed the avogadro and
packmol well,
but I do not know
where the avogadro
Since anybody helped me with this issue and I solved the problem, I'll
report the solution here to contribute with the comunity.
As I pointed in the original e-mail, the problem was the difference
between the numbering scheme of .gro file and .itp file.
I created 3 .pdb files, one for each
Hi all,
I am using CHARMM forcefield with tables for Protein SOL interactions for
alanine dipeptide.
Tables supplied: table.xvg, table_Protein_SOL.xvg, tablep.xvg (Standard
tables for 6-12 interactions used)
Combination rule changed from '2' to '1' in forcefield.itp file.
In the energy
Hi everyone, I met a problem in the installation of gromacs-4.5. There isn’t any mistake in the configuration step, but in the “make” step, it exit with the error: make[4]: *** No rule to make target `/usr/incluDe/gnu/stubs-64.h', needed by `sgetri.lo'. Stop. make[4]: Leaving directory
Hello,
I am trying to rotate my protein in my simulation box (solvent molecules
are there as well). I issue the following command:
editconf_d_mpi -f AFPIII_Ih0001_54_26_em.gro -n protein.ndx -rotate 15
180 0 -o AFPIII_Ih0001_54_26_rotated.gro -box 5.40022 6.23564 20.59328
I select my group
On 19/10/2010 8:11 AM, Paymon Pirzadeh wrote:
Hello,
I am trying to rotate my protein in my simulation box (solvent molecules
are there as well). I issue the following command:
editconf_d_mpi -f AFPIII_Ih0001_54_26_em.gro -n protein.ndx -rotate 15
180 0 -o AFPIII_Ih0001_54_26_rotated.gro -box
Payman Pirzadeh wrote:
After rotation, wouldn't a minimization with very very small steps solve the
problem?
If any atoms overlap, you can't count on this working. It would be hit or miss.
The proper way to build the system would be to orient the solute, then fill
the box with solvent.
On 19/10/2010 12:22 PM, Payman Pirzadeh wrote:
After rotation, wouldn't a minimization with very very small steps solve the
problem?
Only if the solute surface was very close to being symmetric about the
rotation axis. Since that never happens, editconf doesn't even have the
ability to try.
Dear Mark and Justin,
Thanks for very informative comments. I'll try to rotate and then solvate.
Paymon
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Mark Abraham
Sent: October 18, 2010 7:26 PM
To: Discussion list for GROMACS
Hi
According to the following website,
http://en.wikipedia.org/wiki/Bond_dipole_moment
[image: \mu = \delta \, d].
The bond dipole is modeled as +δ -- δ- with a distance *d* between the partial
charges http://en.wikipedia.org/wiki/Partial_charges +δ and δ-.
For a complete molecule the total
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