1) Ensure that lipid_posres.itp was included in the topology by using grompp
-pp processed.top
2) Check the content of lipid_posres.itp (often the P-atoms are restraint only
and not the tails), you may post an extract of that file to the mailing list.
Andreas
From:
This a PhD position suitable for EU or UK permanent residents only:
Part-time PhD combined with Technical Officer at the University of
Hertfordshire, United Kingdom, closing date 3rd of January 2012
In the area of bioinformatics/computational biochemistry/computational biology
£8112 - £9910 per
Hello,
Firstly, proper equilibration is a technical requirement. The production MD
simulation might crash, if the system was not properly equilibrated.
Secondly, if you want to study the properties of a macromolecule in solvent,
you must do a macromolecule position-restraint equilibration.
Justin A. Lemkul jalem...@vt.edu wrote:
Lara Bunte wrote:
Yes it was included in forcefield.itp
Only pdb2gmx uses .rtp files (see the manual).
Thanks for your help
Know I got the error
No default Fourier Dih. types
What should I do?
You need a corresponding [dihedraltypes] for
Hi,
You need make_ndx: http://manual.gromacs.org/online/make_ndx.html
This command gives you an interactive dialogue, in which you can select the
atoms/residues/molecules you want to include in the index file. The selection
is a bit tricky, but using the help function and looking at examples
Hello,
Upon continuing a replica exchange MD simulation using the command
mdrun -cpi state.cpt -append -s tpr_remd20ns_.tpr -multi 48 -replex 1 -cpt
60 -x xtcRemd_20ns.xtc -c afterRemd_20ns.gro -g logRemd_20ns.log -v -e
edrRemd_20ns.edr -stepout 2000
I get the following output:
It is possible that the system is unstable/exploding due atoms being too close
to each other in the initial system.
Andreas
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of Gavin Melaugh
Sent: 21 March 2012 15:45
To: Discussion
Hi Francesco,
It should be the same ensemble, in which you want to carry out the production
REMD.
Andreas
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of francesco oteri
Sent: 23 March 2012 09:41
To: Discussion list for GROMACS users
Subject:
GROMACS can do QM/MM.
Andreas
---
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of Farzad Molani
Sent: 17 November 2009 08:57
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] access code for qmmm
Hello,
Have you ever
That info is in the GROMACS manual - a very nice manual with lots of effort put
in to answer such questions.
A.
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of subarna thakur [thakur.suba...@yahoo.co.in]
Sent: 25 November
Hi all,
When I look at the trajectory of a lipid/protein/water system generated with
Gromacs 4.05 on four cores, the lipid bilayer looks messed up with bonds drawn
all over the system, while the protein and water are displayed correctly.
This is similar to previous Gromacs3 trajectories that
visualisation with VMD
Kukol, Andreas wrote:
Hi all,
When I look at the trajectory of a lipid/protein/water system generated
with Gromacs 4.05 on four cores, the lipid bilayer looks messed up with
bonds drawn all over the system, while the protein and water are displayed
correctly
Hi,
Lipid parameters for Gromos96 53a6 are available based on the publication
Kukol, A., 2009. Lipid models for united-atom molecular dynamics simulations of
proteins. J. Chem. Theor. Comput.,5(3), 615-626.
Unfortunately, I did not manage yet to upload it on the new Gromacs website.
Please
I recall that somewhere on the Gromacs website is the Drug-Enzyme tutorial by
Kerrigan. That is what you are looking for.
Andreas
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Rohit Farmer
Sent: 16 February 2010 08:33
To:
If you are new to Gromcs you must study all the documentation/tutorials/HowTo's
first, in particular this one about parametrization of new molecules:
http://www.gromacs.org/Documentation/How-tos/Parameterization
Andreas
---
From: gmx-users-boun...@gromacs.org
My sincere apologies for this inappropriate message: Attached is an advert for
a combined Senior Technical Officer/PhD position, deadline 30th of April
Best wishes
Andreas
HH9068ad.pdf
Description: HH9068ad.pdf
--
gmx-users mailing listgmx-users@gromacs.org
Hi,
The POPC_53a6 topology works only with Gromacs versions lower than 4. Please
find attached the topology compatible with Gromacs4.
I shall update files on the Gromacs website. Sorry for causing confusion.
Best wishes
Andreas
From:
Alex,
I used the membrane builder and even developed a script to convert that POPC
into Gro53a6 - please contact me by personal email, if you want it.
Afterwards I found, that the resulting protein/lipid system contained many
overlaps between atoms and removing all the overlaps created a
Hi,
I am not exactly sure about your question, but for lipids and membrane
composition there are several books about lipids e.g. The Lipid Handbook
'Biomembranes' by Gennis.
A good source for topologies (itp-files) is:
http://lipidbook.bioch.ox.ac.uk/
Best wishes
Andreas
-Original
Use the Gromacs program genion for that purpose. This replaces water molecules
by the ions you specify. You may need to change the topology afterwards
manually. Make sure, you put an #include ions.ipt near the top of the
.top-file, this contains the force field parameters for ions.
Best wishes
Hi,
Autodock4 uses the AMBER forcefield, so that would be a good starting point for
gromacs as well.
In order to set the temperature for a particular group
1) you generate an index file containing all the atoms in your GROUP
2) in your mdp-file specify GROUP as a separate temperature coupling
You have to modify the input .mdp and run grompp again. The mdout.mdp is for
information only.
Andreas
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of Andrea Muntean
Sent: 10 November 2008 12:42
To: Gromacs Users' List
Subject: [gmx-users] .mdp
Yes, it is possible by deveoping your own topology. Pdb2gmx is not suitable for
that purpose.
It would be helpful to check out the documentation resources and manual, e.g.
http://wiki.gromacs.org/index.php/FAQs
x2top and the prodgr web-server might be some good starting points.
Andreas
Hello,
Is there any way to extract the diagnonal from an xpm matrix ?
What I am trying to do, is to calculate the RMSD between two trajectories using
g_rms:
g_rms -s topol.tpr -f traj1.xtc -f2 traj2.xtc -m rmsd.xpm
and the RMSD at the same time points is supposed to be the diagonal of the
Tcl is not part of Gromacs. Please direct your enquiry to the appropriate
mailing list, e.g.
http://www.tcl.tk/community/
Andreas
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of varsha gautham
Sent: 20 January 2009 07:05
To: gmx-users@gromacs.org
I have no experience with polyalanine, but you may try position restraint MD
for longer (500 ps) and energy minimisation of the the whole system afterwards.
Andreas
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of li jianguo
Sent: 22 January 2009 05:39
Dear Caty,
You have to make an index file containing groups for each type of atom in one
of your tails (e.g. the sn1-chain), that means for dppc you end up with 15
groups: C11, C12, C13, ...
Each group will have 100 elements.
For the sn2-chain you need to make a separate index file.
Andreas
Dear all,
Please find topologies (.itp files) for the lipids DPPC, DMPC, POPC and POPG
for the GROMOS96 53a6 force field in the User
Contributions-Downloads-Topologies-Molecule Topologies section
When using these files please cite:
Kukol, A., 2009. Lipid models for united-atom molecular
Apparently the final mdrun has not worked successfully. It would be interesting
to see what the system looks like after the position restraint mdrun.
Andreas
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of Pawan Kumar
Sent: 06 April 2009 07:47
To:
:11 PM, Kukol, Andreas a.ku...@herts.ac.uk wrote:
Apparently the final mdrun has not worked successfully. It would be interesting
to see what the system looks like after the position restraint mdrun.
Andreas
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf
Hello,
Is it possible to globally scale all non-bonded interactions by a factor ? I
know there are energy exclusion groups, but that is an all or nothing approach,
while I would like to reduce non-bonded interaction potentials to e.g. 10% of
their normal value.
If this is not possible, I
Use trajcat with the option -settime then you can specify the starting time for
each simulation interactively.
Andreas
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Miguel Quiliano Meza [rifaxim...@gmail.com]
Sent: 01
Hello,
Is there any way to output the dipole moment averaged over all molecules or for
each molecule separately (and not the total dipole moment of the simulation
box) ?
Apparently the dipole autocorrelation function can be obtained as an average
over all molecules with the '-corr mol'
] g_dipoles - averaging
On Thu, 2011-08-04 at 09:08 +0100, Kukol, Andreas wrote:
Hello,
Is there any way to output the dipole moment averaged over all molecules
or for each molecule separately (and not the total dipole moment of the
simulation box) ?
Yes, the tool g_current decomposes
Dependent on the force field you are using, the topology of free amino acids
may not be defined. Look at the content of the rtp-file for your forcefield, if
the free amino acid is defined there, you can use pdb2gmx to generate the
topology.
Otherwise you have to treat the amino acid as a new
Yes, that will be enough.
Andreas
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Ragothaman Yennamalli [ragotha...@gmail.com]
Sent: 10 August 2011 20:35
To: Discussion list for GROMACS users
Subject: [gmx-users] running
I don't think there is that possiblity, because protein diffusion is a natural
process that occurs in your simulation.
Andreas
---
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of Birgit Hischenhuber
Sent: 01 June 2010 15:24
To:
-Ursprüngliche Nachricht-
Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im
Auftrag von Kukol, Andreas
Gesendet: Dienstag, 1. Juni 2010 16:49
An: Discussion list for GROMACS users
Betreff: RE: [gmx-users] Visualizing of a peptide in a water box
Including Fe2+ should not be very difficult, look at the definitions for Cu2+
or others in ffG53a6.nb or any other forcefield you want to use. You need to
find the correct Lennard-Jones parameters C6 and C12 and then validate your
model.
I am not sure, what the FES molecule is, but developing
Yes, that is an interesting question. I don't know the answer, but is there any
way to get the numerical values of the matrix from Gromacs tools that produce a
matrix in xpm format ? I have problems with g_rms and g_rmsdist is another
candidate.
Andreas
-Original Message-
From:
Hi,
I am using g_cluster to analyse a trajectory (protein backbone):
g_cluster -f traj.xtc -s topol.tpr -g cluster.log -skip 10 -cutoff 0.5 -fit
-method linkage
As a result I get almost hundred clusters. The plot of the RMSD against time
for the same trajectory generated with g_rms shows a
Try without -DFLEXIBLE.
See this message:
http://lists.gromacs.org/pipermail/gmx-users/2008-October/037571.html
Andreas
---
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of NG HUI WEN
Sent: 20 September 2010 04:21
To:
You find those definitions in ffG43a1bon.itp. As far as I know, they are simply
placeholders for the explicit data. Probably you can insert the explicit data
into the rtp file.
Andreas
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of Mattia Sturlese
Hi,
Does anyone know which atom and bond types to use for a carbon double bond in a
simple organic molecule like RCH=CHR in the Gromos 53a5 forcefield ?
Is it CH1 or CR1 ?
Bond type gb_10 ?
Angle bending CH2-C=C parameters ?
Improper dihedral should be gi_1
The original publication
This will be helpful for you:
http://wiki.gromacs.org/index.php/Exotic_Species
and other information from gromacs wiki.
Andreas
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of s lal badshah
Sent: 16 April 2008 11:12
To: gromacs
Subject: [gmx-users] Error in topology file
Dear
Hi,
First note that 0.658 is in nm^2 per lipid, while you quoted the box dimensions
in Angstrom.
If you include the standard error of 0.009 nm^2, you will see that box size of
the snapshot is within the error margin. The standard error is the sample
standard deviation divided by sqr(N), with
Use the -res option for g_rmsf to calculate the average for each residue. But
beware: the experimental B-factor is defined for atoms.
Andreas
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Alif M Latif
Sent: 02 May 2008 09:42
To: gmx-users@gromacs.org
Subject: [gmx-users]
1) You need to include ions.itp in your topology file:
#include ions.itp
2) Make sure, you include the correct name for the atom in the systems section
of your topology file:
For gromos96 forcefield variants this is 'CL-'
Good luck
Andreas
-Original Message-
From: [EMAIL PROTECTED]
This book is out now:
Molecular Modeling of Proteins
# Hardcover: 396 pages
# Publisher: Humana Press; 1 edition (February 19, 2008)
# Language: English
# ISBN-10: 1588298647
# ISBN-13: 978-1588298645
Here is a list of contents:
Methodology
1 Molecular dynamics simulations
Erik R. Lindahl
2
Check out ffG53a6.rtp (in gromacs/share/gromacs/top) for the atom name
requirements for urea, the residue name is UREA. This and other files therein
will also give you an idea how gromos96 files look like.
For the small alkane chain, you need to make an .itp file and include it in
your
You need to create your topology file manually and have a look at this:
http://wiki.gromacs.org/index.php/Exotic_Species
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of RAJAVARMAN.K
Sent: 09 May 2008 15:34
To: gmx-users@gromacs.org
Subject:
Use -b and -e options repeatedly to save part of your trajectory into a series
of files
OR: use '-skip 2' to reduce the number of frames by half over the whole of your
simulation.
Andreas
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of serdar durdagi
Sent: 13 May 2008 08:16
To:
First try the EM/MD of 1 molecule in vacuum ('ethanol-gas') and check, if it
looks reasonable.
You could also have a look at the definition of ETHH in the GROMOS96
forcefield, e.g. in ffG43a2.rtp. Although this is a united atom topology it
might give you clues, if something is wrong.
Andreas
minimisation problem
On Tue, 2008-05-13 at 20:32 +0300, Jussi Lehtola wrote:
On Tue, 2008-05-13 at 14:34 +0100, Kukol, Andreas wrote:
First try the EM/MD of 1 molecule in vacuum ('ethanol-gas') and check,
if it looks reasonable.
Thanks, using the vacuum method I seem to get better results
The snapshots are saved automatically during the simulation in the trajectory,
e.g.
mdrun ... -x trajectory.xtc
How often snapshots are saved depends on the settings in your .mdp-file.
I recommend some reading of the manual before starting any simulations.
Regards
Andreas
From: [EMAIL
First, make an index file that contains one group each for every carbon atom in
the acyl-chain (starting with the carbonyl-carbon and going further down).
You need to make two index files: for sn1 and sn2 chains of DPPC
Then you get the deuterium order parameters for each atom with the output
Dear Anirban,
In order to answer your first question about sn1/sn2 chain, you should do some
background reading about the molecular structure of phospholipids and look at
some experimental or simulation papers, where order parameters have been
reported.
In order to make the index file, you
Your output looks like, that you are doing MD simulations, because a time in ps
is reported. You should do energy minimisation first, use 'integrator = steep'
in your .mdp file
Andreas
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of [EMAIL
Yes that should be possible without big problems. The Gromacs manual and Wiki
pages about how to build a topology is a good starting point.
Then you could try the gromacs program x2top to generate a topology, or the
Prodrg2 server.
Andreas
-Original Message-
From: [EMAIL PROTECTED]
mpirun -np number of processors mdrun various options... -np number of
processors
(all in one line)
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of vivek sharma
Sent: 20 August 2008 12:44
To: Discussion list for GROMACS users
Subject: [gmx-users] MDRUN with MPIRUN
Hi There,
I
Hello Rolf,
There might be some issues with the exact format, below I pasted a record from
a standard pdb-file (that works with pdb2gmx) for comparison.
Otherwise for a simple molecule like methane, x2top is probably better suited
than pdb2gmx to generate the topology.
Best wishes
Andreas
Dear all,
I included the following dihedral potential function in a topology:
V(phi2) = -5.865 + 7.470 [1+cos(phi2-180°)] + 3.99 [1+cos(2 phi2)] + 1.1
[1+cos(3 phi2-180°)]
The problem is about representing the constant term -5.865. Using equation 4.61
(Gromacs 4.0 manual):
V(phi) = k * (1 +
Hi,
I supply the multiple dihedral terms as a combination of single ones, such as:
;atom no. type phisk mult
22232425 11807.470 1
22232425 10 3.900 2
22232425 11801.100 3
222324
It is not straightforward to use the AMBER forcefield with Gromacs. You need to
edit your pdb-file to account for different atom/residue names used by AMBER as
opposed to GROMOS forcefields.
Detailed info is here: http://chemistry.csulb.edu/ffamber/
If this is your first MD simulation, try
As you already pointed out, it may take a very long time on ordinary PCs. On a
laptop it would take even longer ...
Use a Linux workstation with 4 processor cores minimum.
Andreas
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf
It is not very difficult to construct a topology (itp-file) for one atom. You
may look at the definitions of sodium or chloride in the .rtp file for the
force field you want to use and adapt them to your needs.
Then you need the atom coordinates of the two parallel lattices, which you can
make
The exact functional forms are given in the Gromacs manual, most likely in one
of the earlier chapters.
Andreas
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of AverettDevin [daver...@wisc.edu]
Sent: 26 June 2009 22:42
To:
Bing Bing,
There is a topology available for POPC with ffG53a6 in the user contribution
section.
Published in: Kukol, A., 2009. Lipid models for united-atom molecular dynamics
simulations of proteins. J. Chem. Theor. Comput.,5(3), 615-626.
However, it currently doesn't work with Gromacs 4,
Dear all,
I get the following grompp error message with Gromacs 4.05 (but not with
Gromacs 3.2.1):
...
Opening library file /usr/local/gromacs4/share/gromacs/top/ffG53a6bon.itp
Opening library file /usr/local/gromacs4/share/gromacs/top/ff_dum.itp
Generated 165 of the
You need to specify the name of your input file with the option '-f brady.pdb'
A.K.
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Asmaa Elsheshiny
Sent: 01 October 2009 11:37
To: gmx-users@gromacs.org
Subject: [gmx-users]
Dear all,
I get the following grompp error message with Gromacs 4.05 (but not with
Gromacs 3.2.1):
...
Opening library file /usr/local/gromacs4/share/gromacs/top/ffG53a6bon.itp
Opening library file /usr/local/gromacs4/share/gromacs/top/ff_dum.itp
Generated 165 of the
Apart from specifying -DPOSRES in your mdp file, you need to make sure that
posre.itp will be included into your topology. There is usually a statement
like 'ifdef POSRES ...
Andreas
---
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf
Hi,
Finally I found the reason for the error:
A space is required between the forcefield parameter code and the semicolon
indicating a comment, i.e.:
No default G96Bond types error:
3132 2gb_18; C-O ether bond - line 88
Works fine:
3132 2gb_18 ; C-O ether bond
Yes, everyone knows why this happens. This question has been asked so often
that there is a FAQ on the Gromacs web-site:
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
Best wishes
Andreas
---
From: gmx-users-boun...@gromacs.org
Hello,
Does anyone know if there is a tool called g_saxs available in the latest
version of Gromacs or planned for any future version. It is supposed to compute
small-angle x-ray scattering profiles from trajectories.
Many thanks
Andreas
--
gmx-users mailing listgmx-users@gromacs.org
2013 14:03
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] g_saxs
On 9/4/13 8:55 AM, Kukol, Andreas wrote:
Hello,
Does anyone know if there is a tool called g_saxs available in the latest
version of Gromacs or planned for any future version. It is supposed to
compute
You need to contact your cluster administrator for instructions of how to
submit jobs to the cluster. Usually you have to create some kind of
shell-script that specifies various parameters of your job and then submit it
to a queue system.
Below you submitted the job most likely to the
And apparently you have only 6438 atoms in system_inflated.gro. So that is the
source of the error.
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
boun...@gromacs.org] On Behalf Of hasthi
Sent: 08 October 2013 05:56
To: gmx-users@gromacs.org
Subject:
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