You can use g_order for that with just a bit of additional scripting.
Erik
maria goranovic skrev 2011-05-10 09.17:
So, one can probably do this using a simple script?
for each frame
make index file of water molecules within 0.5 nm using g_select
extract frame based on above selection
done
dear users
while installing gromacs and after running ./configure, i tried to run the
make command. but soon i was faced with an error witch is typed below. it
seems that fftw libraries are not found. i downloaded and installed fftw3.2.2
as
mentioned in gromacs website. and put the extracted
Dear GROMACS users,
I wonder if it is not possible to use more than 1 core (according to the
manual) for each replica using GROMACS 4.0.x?
In the manual is written that the number of cores defined by the -np
option of mpirun has to be the same as the number of replicas.
Thanks
Sebastian
--
On 10/05/2011 5:03 PM, Sajad Ahrari wrote:
dear users
while installing gromacs and after running ./configure, i tried to run
the make command. but soon i was faced with an error witch is typed
below. it seems that fftw libraries are not found. i downloaded and
installed fftw3.2.2 as mentioned
On 10/05/2011 5:36 PM, SebastianWaltz wrote:
Dear GROMACS users,
I wonder if it is not possible to use more than 1 core (according to the
manual) for each replica using GROMACS 4.0.x?
You can use more than one core per replica from 4.0 onwards.
In the manual is written that the number of
On Mon, May 9, 2011 at 6:28 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 10/05/2011 12:50 AM, maria goranovic wrote:
Dear experts
I have a protein simulation in a water box. I now want to write a
trajectory containing only the protein, and water molecules within 5
Angstroms of the
Dear Mark,
i followed the same stuff in the tutoriali created the
table and tried the following command
*
grompp -f em.mdp -p tol.top -c nacl3.pdb*
i got the following etrrors
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Back Off! I just backed up
On 10/05/2011 1:04 PM, sreelakshmi ramesh wrote:
Dear Mark,
i followed the same stuff in the tutoriali created
the table and tried the following command
*
grompp -f em.mdp -p tol.top -c nacl3.pdb*
i got the following etrrors
Ignoring obsolete mdp entry 'title'
Ignoring
Hi,
I want to study the shape change of a macromolecule which seems like a
ellipsoid. So, I need obtain the three principal moments of the molecules.
Is the command of g_gyrate helpful for me? The sum of the three principal
moments should be equal to the Rg^2. However, I used the command
Hi,
BioVEC is a tool for visualizing molecular dynamics simulation data while
allowing coarse-grained residues to berendered as ellipsoids.
http://www.phas.ubc.ca/~steve/BioVEC/BioVECindex.html
2011/5/10 Mark Abraham mark.abra...@anu.edu.au
On 10/05/2011 8:23 PM, lammps lammps wrote:
Hi,
I
Dear users,
I wanted to know when DEFINE = -DFLEXIBLE has to be used.
its given in the manual that it has to be used when we require flexible
water instead of rigid waters, so if I am using tip4p water model and
OPLSAA force field, and i use DFLEXIBLE option in EM and not in
position MD, is
Mark Abraham skrev 2011-05-10 12.31:
On 10/05/2011 8:23 PM, lammps lammps wrote:
Hi,
I want to study the shape change of a macromolecule which seems like
a ellipsoid. So, I need obtain the three principal moments of the
molecules.
Is the command of g_gyrate helpful for me? The sum of the
Kavyashree M wrote:
Dear users,
I wanted to know when DEFINE = -DFLEXIBLE has to be used.
its given in the manual that it has to be used when we require flexible
water instead of rigid waters, so if I am using tip4p water model and
OPLSAA force field, and i use DFLEXIBLE option in EM
Not R_x, R_y, and R_z.
What I want to obtain are the three three principal moments of the
ellipsoidal macromolecule.
They are different quantities.
2011/5/10 Erik Marklund er...@xray.bmc.uu.se
Mark Abraham skrev 2011-05-10 12.31:
On 10/05/2011 8:23 PM, lammps lammps wrote:
Hi,
I want
lammps lammps wrote:
Not R_x, R_y, and R_z.
What I want to obtain are the three three principal moments of the
ellipsoidal macromolecule.
They are different quantities.
Then isn't g_principal the more appropriate tool, rather than g_gyrate?
-Justin
2011/5/10 Erik Marklund
Thanks
With Regards
Kavya
On Tue, May 10, 2011 at 5:32 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Kavyashree M wrote:
Dear users,
I wanted to know when DEFINE = -DFLEXIBLE has to be used.
its given in the manual that it has to be used when we require flexible
water instead of
Yes,
However, what does the data in axis1.dat, axis2.dat, axis3.dat and moi.dat
mean?
Should I put the center-of-mass of the molecule in the origin when using the
g_principal command?
It seems that the inertia is calculated relative to the origin. May be my
understanding wrong.
--
wade
--
lammps lammps wrote:
Yes,
However, what does the data in axis1.dat, axis2.dat, axis3.dat and
moi.dat mean?
Should I put the center-of-mass of the molecule in the origin when using
the g_principal command?
It seems that the inertia is calculated relative to the origin. May be
my
Thank you for your informative reply, Sir,
Now I understood the problem but when i was tried with another ligand (GSSG)
It could be simulated. Later I found error for different ligand.
please give me the solution, what sort of force field should be applied?
On 9 May 2011 21:27, ITHAYARAJA
Hi,
There have been reports about inconsistencies between older (= 4.0.7?)
and newer versions of g_hbond, where the older seem to have been more
reliable. I found and killed the bug that caused the newer versions to
miscount the hbonds. Checkout release-4-5-patches to get the bugfix, or
ITHAYARAJA wrote:
Thank you for your informative reply, Sir,
Now I understood the problem but when i was tried with another ligand
(GSSG) It could be simulated. Later I found error for different ligand.
So some systems work and others don't. You haven't described what you're doing,
or
Dear Gromacs user,
my intel compiler issue got solved with a combination off autoconfiger and
cmake. In a first step, I used autoconfigure for FFTW-3.2.2 and solved my
compilation/segfault problems for gromacs-4.5.4 with cmake:
##For FFTW compilation ##
./configure --enable-threads
Dear GROMACS users,
Does someone now how to procede to change the pH of a MD simulation
from the physiologic one (7.4) to 6.5 ?
Tanos Celmar Costa Franca - D.Sc
Coordenador do Programa de Pos-graduacão em Química
Secão de Engenharia Química - SE/5
Instituto Militar de Engenharia - IME
Rio
Tanos Celmar Costa Franca wrote:
Dear GROMACS users,
Does someone now how to procede to change the pH of a MD simulation from
the physiologic one (7.4) to 6.5 ?
Classical MD simulations do not currently allow for dynamic proton exchange.
The best you can do at the moment is use pdb2gmx
Hi All
I have set up a topology file and with virtual sites (exerpts below),
whereby my virtual sites only interact with the C3 atoms. I am trying to
construct a PMF wrt one particular C3. This atom I do not want to
interact with the virtual sites at all. I thought the best way to do
this was via
Hi again
To rephrase. If I have two atoms constructing a charge group, is it not
possible to have one of these atoms constructing an energy group on its own?
Cheers
Gavin
Gavin Melaugh wrote:
Hi All
I have set up a topology file and with virtual sites (exerpts below),
whereby my virtual
Dear GROMACS User,
I'm running a REMD MD of 32 replicas. It worked for the first few
replica exchanges. After 30ps again two replicas were exchanged and I
received the Error:
x particles communicated to PME node y are more than a cell length out
of the domain decomposition cell of their charge
Hi all
Do atoms belonging to the same charge group have to be indexed
consecutively in the topology file or can you have the following.
[atoms]
1 CA 1 CGECA 1 -0.1150 12.0110
2 CB 1 CGECB 1 0. 12.0110
3
Hi Tanos,
Perhaps you should try one of the available constant-pH MD methods. Here is
a quick explanation of what they do and who is involved in their development
right now:
http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation
My opinion regarding this subject may be a little
Gavin Melaugh wrote:
Hi again
To rephrase. If I have two atoms constructing a charge group, is it not
possible to have one of these atoms constructing an energy group on its own?
You can't split charge groups, per the error you posted before.
-Justin
Cheers
Gavin
Gavin Melaugh wrote:
Gavin Melaugh wrote:
Hi all
Do atoms belonging to the same charge group have to be indexed
consecutively in the topology file or can you have the following.
[atoms]
1 CA 1 CGECA 1 -0.1150 12.0110
2 CB 1 CGECB 1 0.
I have a pure linux question. When using g_current and trying to
redirect its output to the file, e.g.
g_current -temp $TEMPER -b $conduct_b -e $conduct_e EOF output
0
EOF
only a part of output is written to the file (output)
Here is what is actually written to the file:
Selected 0: 'System'
Vitaly Chaban wrote:
I have a pure linux question. When using g_current and trying to
redirect its output to the file, e.g.
g_current -temp $TEMPER -b $conduct_b -e $conduct_e EOF output
0
EOF
only a part of output is written to the file (output)
Here is what is actually written to the
Gavin Melaugh wrote:
Hi Justin
The two files processed.top and topol.top are the exact same. What is
worrying me is that when I look at the topol.tpr from gmxdump, my charge
groups do not seem to be specified the way I stated in the topology file.
Can you provide a relevant snippet of the
As you can see atomnr 7 HC should belong to the same charge group (1) as
atomnr 12. From the tpr file atomnr 7 (in this file 6) seems to have
its own charge group (3).
[atoms]
; atomnr type resnr residue namecgnr charge mass
1 CA 1 CGECA 1
Hi,
Good that managed to solve the issue!
Even though it might have been caused by a bug in the autoconf
scripts, as these are the final days for the autoconf support in
Gromacs, I see a very slim change that it will get
investigated/fixed.
--
Szilárd
On Tue, May 10, 2011 at 4:19 PM,
Gavin Melaugh wrote:
As you can see atomnr 7 HC should belong to the same charge group (1) as
atomnr 12. From the tpr file atomnr 7 (in this file 6) seems to have
its own charge group (3).
[atoms]
; atomnr type resnr residue namecgnr charge mass
1 CA 1 CGE
O.K cheers
I assume that this is irrelevant in vacuum with no cut-offs
Gavin
Justin A. Lemkul wrote:
Gavin Melaugh wrote:
As you can see atomnr 7 HC should belong to the same charge group (1) as
atomnr 12. From the tpr file atomnr 7 (in this file 6) seems to have
its own charge group (3).
Gavin Melaugh wrote:
O.K cheers
I assume that this is irrelevant in vacuum with no cut-offs
Or (for reference) with PME, I would suspect, since in this case charge groups
do not have to be net neutral.
-Justin
Gavin
Justin A. Lemkul wrote:
Gavin Melaugh wrote:
As you can see atomnr
Just some hints:
- Does the target platform (32/64 bit) or the fftw libs and Gromacs
build match?
- Try to do a make clean first and (/or?) and reconfigure with
--enable-shared. Not sure that it will help, but I vaguely remember
something.
- Try CMake.
Cheers,
--
Szilárd
On Tue, May 10,
Also. Obviously I arranged the charge groups like this so that they
would be neutral, I just didn't realise that the atoms comprising the
charge groups had to be in sequence.
Justin A. Lemkul wrote:
Gavin Melaugh wrote:
As you can see atomnr 7 HC should belong to the same charge group (1) as
Thanks, Justin! Great solution.
On Tue, May 10, 2011 at 12:57 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Vitaly Chaban wrote:
I have a pure linux question. When using g_current and trying to
redirect its output to the file, e.g.
g_current -temp $TEMPER -b $conduct_b -e $conduct_e EOF
Frank Neuhaus wrote:
Hi,
I have a protein simulation in which all residues simulate correctly
with the exception of five in a loop. These five out of 360 are in a
loop (or bend) separate from my area of interest. Thus, I would like to
treat them as a rigid sequence. Using the position
The gmx-developers list is not the forum for these types of questions. I am
replying via gmx-users, which is where the discussion should stay.
I took a few minutes to dig into this. My conclusion is that your system is not
stable. I would encourage you to analyze the temperature and
Hi gmxers,
I am working on qmmm treatment of a heat shock protein. Heat-sensitive part is
treated quantum mechanically, while the other parts classically.
I am hence wondering if it is available and applicable in gromacs that this qm
part can be heated and cooled for temperature variation
Hi gmxers,
I am just wondering how to give a linking atom's coordinates in a qmmm
calculation generally.Would it be normal to take an arithmetic average of two
neighboring qmmm-layer-bonding atoms' coordinates?
Thanks,
Yao
--
gmx-users mailing listgmx-users@gromacs.org
On 05/11/2011 08:15 AM, Yao Yao wrote:
Hi gmxers,
I am working on qmmm treatment of a heat shock protein.
Heat-sensitive part is treated quantum mechanically, while the other
parts classically.
I am hence wondering if it is available and applicable in gromacs that
this qm part can be heated
On 05/11/2011 06:24 AM, Frank Neuhaus wrote:
Hi,
I have a protein simulation in which all residues simulate correctly
with the exception of five in a loop. These five out of 360 are in a
loop (or bend) separate from my area of interest. Thus, I would like
to treat them as a rigid sequence.
On 05/11/2011 02:32 AM, SebastianWaltz wrote:
Dear GROMACS User,
I'm running a REMD MD of 32 replicas. It worked for the first few
replica exchanges. After 30ps again two replicas were exchanged and I
received the Error:
x particles communicated to PME node y are more than a cell length out
of
On 05/11/2011 02:04 AM, Gavin Melaugh wrote:
Hi again
To rephrase. If I have two atoms constructing a charge group, is it not
possible to have one of these atoms constructing an energy group on its own?
Correct. Neighbour lists are constructed from the set of whole charge
groups in each
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