Dears,
the MARTINI CG force field web site has been remodeled.
It now includes FAQs, tutorials, a forum and much more ...
http://md.chem.rug.nl/cgmartini
Enjoy.
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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
It is documented. Have a look at this one:
Dirk Matthes and Bert L. de Groot. Secondary structure propensities
in peptide folding simulations: A systematic comparison of molecular
mechanics interaction schemes. Biophys. J. 97:599-608 (2009)
Erik
XAvier Periole skrev:
The instability of helices
The instability of helices with the G53a6 force field is definitely real
and unfortunately not documented. Some people are working on it ...
I would advise to be very carefull in interpreting results with this FF.
XAvier.
On Jan 21, 2010, at 2:13 PM, Justin A. Lemkul wrote:
Krzysztof
You can use spc216.gro ... they have basically the same structure.
You could also equilibrate the spc216.gro file with your tip3p setup.
On Jan 19, 2010, at 7:28 AM, Yang Ye wrote:
You may find it in gromacs source.
On Tue, Jan 19, 2010 at 2:08 PM, xiao shijun xshi...@gmail.com
wrote:
Hi
Pharmacy and Pharmaceutical Sciences
Monash University
A polar bear is a Cartesian bear that has undergone a polar
transformation
-Original Message-
From: gmx-users-boun...@gromacs.org on behalf of XAvier Periole
Sent: Tue 1/5/2010 6:33 AM
To: Discussion list for GROMACS users
Subject
It is always better to keep the discussion in the list. Someone
could benefit of it as well as you from others.
From: Lum Nforbi lumngwe...@gmail.com
Date: January 4, 2010 7:57:04 PM GMT+01:00
To: XAvier Periole x.peri...@rug.nl
Subject: Thank you for reply on RDF PLOT problem/Question.
Hi
I am not sure somebody gave you an answer ...
the first intense and probably very narrow pick is very
likely due to the intramolecular OH distance. It should be
around 0.1 nm, isn't it?
On Jan 1, 2010, at 3:53 AM, Lum Nforbi wrote:
-- Forwarded message --
From: Lum Nforbi
what is difference between rmsd and rmsf?
obviously, one has a d at the end while the other has a f !
google would tell you all about it!
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gmx-users mailing listgmx-users@gromacs.org
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Please search the archive at
From what my Professor told me it is my understanding that cutoff
length is somewhat a trade-off between accuracy of the simulation
and length of time to generate the simulation. A higher cut-off
indicates more accuracy but will take longer to simulate. I use low
cut-offs for less
Would it be all cut-offs: elect + vdW ? Or the increase is separate?
For your info the vdW are attractive potentials at long distances so
an increase of cutoff would result in an increase of attraction and
therefore to an increase of density!
This is one good illustration of the fact that you
Dears,
we have been trying to run gmx-4.0.X on new machines with the
Intel I7 CPUs. It is a quad core intel on which multi-threading is
a default feature. This makes the system to behave as a 8 cores
machine.
We observed some strange behavior of gromacs. Note that is
certainly not due to
Is this a real gromacs-user question?
Have your tried to contact the MArtini developers?
As a matter of fact some of them have prepared a new MARTINI
web-site where a discussion forum will be on.
To answer your question: using MARTINI for the unfolding
mechanism of proteins would be very
try the option -ignh, it will ignore the the hydrogen atoms in your
pdb file and generate the ones necessary to the force field you choose.
On Dec 15, 2009, at 9:52 AM, ashish pandey wrote:
Dear all,
my self ashish and i am trying to dynamics using gromacs.
i am new in these
I have downloaded the 128 DPPC lipid molecules from Dr. Tielmen's
Website and I am trying to convert the Atomistic structure to CG
structure. For that I am using atom2cg script provided by the
martini folks but it doesn't convert the Atomistic structure to CG
structure. atom2cg script
, XAvier Periole x.peri...@rug.nl
wrote:
I have downloaded the 128 DPPC lipid molecules from Dr. Tielmen's
Website and I am trying to convert the Atomistic structure to CG
structure. For that I am using atom2cg script provided by the
martini folks but it doesn't convert the Atomistic structure
, 2009 at 12:12 PM, XAvier Periole x.peri...@rug.nl
wrote:
No need of position restrained simulation with the CG lipids.
CG is very forgiving :))
For proteins it is more delicate.
On Dec 15, 2009, at 6:02 PM, sunny mishra wrote:
Thanks for the reply. I have another quick question that If I have
is a combination of CG protein and
CG lipid).
On Tue, Dec 15, 2009 at 12:16 PM, XAvier Periole x.peri...@rug.nl
wrote:
Well if you put a protein CG into your DPPC bilayer you'll have to
be soft on the start. PR is one way to do it and you can do similar
to when doing on a atomistic
On Dec 14, 2009, at 6:08 PM, Nilesh Dhumal wrote:
Hey All,
I am running simulation for 20 ns. My simulation got crashed after
171
steps. I continiued the simulation with following command.
tpbconv -s 3.tpr -o 3n.tpr
this step is not needed you can use the same tpr in your following
On Dec 9, 2009, at 11:21 PM, César Ávila wrote:
Dear all,
I would like to simulate a DPPC membrane in gel phase using Martini
Force Field. As stated on
Simulation of gel phase formation and melting in lipid bilayers
using a coarse grained model, CPL 135 (2005) 223-244
the correct 30º
On Dec 9, 2009, at 3:41 PM, Justin A. Lemkul wrote:
Henry Yang wrote:
Hi there,
Thanks for telling how to calculate the area per lipid. But at the
same time if I want to draw a plot of area per lipid vs time then
how can I proceed? Any gromacs tool comes out which I can use?
thanks
One solution would be to use tabulated potential for which the
analytical form does not matter.
On Dec 8, 2009, at 4:29 AM, Mark Abraham wrote:
hong bingbing wrote:
Dear all,
Has anyone tried to use 2 van de Waals interaction types in one
system? For example, the system includes two
No, unfortunately.
On Dec 6, 2009, at 19:06, Hans HEINDL hhei...@terra.es wrote:
Are there forcefield parameters available for DNA coarse grain
simulations
(ideally the forcefields should be compatible with the Martini cg
parameters
Thanks in advance
Hans HEINDL
--
gmx-users mailing
The message is clear, the program does not find the files (trr) anymore.
This is expected and trying to understand why it does so seems not
really
useful. Especially because erasing an output file while the program is
running is non-sense, although it might be necessary.
Just use the 0
you can define the frequency of writing to the trr file in the mdp file.
using:
nstxout = 0
nstvout = 0
nstfout =0
should fix your problem.
On Dec 1, 2009, at 4:30 PM, Jörn-Benjamin Lenz wrote:
dear users of gromacs,
i updated my gromacs from 4.0.1 to 4.0.5 and now i am facing the
you do not need itp file. in the top you'd find the parameters for
the water.
On Dec 1, 2009, at 6:26 PM, Francesco Pietra wrote:
I forgot to ask, in additio to below, where to find the .itp file for
cg water. All that I have is water.gro water.mdp water.top from the
martini web site.
On Dec 1, 2009, at 6:33 PM, XAvier Periole wrote:
you do not need itp file. in the top you'd find the parameters for
the water.
I mean in the top file you'll find the reference to the martini??.itp
file
where the water is defined.
On Dec 1, 2009, at 6:26 PM, Francesco Pietra wrote:
I
frame
onwards)? So the procedure should work if the reference structure is
the second frame? I have tried that, and it fails as well.
On Thu, Nov 5, 2009 at 4:40 PM, XAvier Periole x.peri...@rug.nl
wrote:
The nojump option will not apply the pbc when an atom is crossing the
box boundaries
attaching my .gro file. If you
find any time, please have a look at it and comment.
Thank you once again.
Regards,
On Sat, 2009-10-31 at 10:49 +0100, XAvier Periole wrote:
Dear Anirban,
Your mdp file seems fine to me.
If I were you I would look at the system. It probably contains bad
contacts between
On Nov 2, 2009, at 18:13, Paymon Pirzadeh ppirz...@ucalgary.ca wrote:
Hi Tom,
Thanks for the tip. It worked on the command line and I had 3000
frames.
But when I fed the file to VMD, it showed only 1800 frames!? Although
the initial and final configurations looked correct. I still am not
for each group.
XAvier.
On Oct 29, 2009, at 11:11 PM, Michael Lerner wrote:
On Thu, Oct 29, 2009 at 5:31 PM, XAvier Periole x.peri...@rug.nl
wrote:
On Oct 29, 2009, at 9:26 PM, Michael Lerner wrote:
I calculated temperatures with
g_traj -f md2.trr -s md2.tpr -n index.ndx -ot -ng 5
I did
On Oct 29, 2009, at 9:26 PM, Michael Lerner wrote:
Hi,
I'm using GROMACS 4.0.5 to do a MARTINI simulation of a CG protein
in a CG water box, looking at the diffusion constant of the protein
among other things. I'm using the Nose-Hoover thermostat and
Parrinello-Rahman barostat with
It is not clear what you actually want to do!
1- You want to generate a topology for MARTINI: follow
the tutorial, which I believe is clear.
2- you want to play with the reverse transformation. For a
protein I believe that there is a parameter file that contains
the CG-AA mapping. For other
On Oct 22, 2009, at 11:28 PM, Amit Choubey wrote:
On Thu, Oct 22, 2009 at 9:53 AM, S hv sola...@hotmail.com wrote:
Hi,
I am currently working with peptide/lipids interactions using the
martini force field. I want to built a bacterial membrane, so I
trying to find the
topology of the
On Oct 23, 2009, at 9:45 AM, Amit Choubey wrote:
On Fri, Oct 23, 2009 at 12:33 AM, XAvier Periole x.peri...@rug.nl
wrote:
On Oct 22, 2009, at 11:28 PM, Amit Choubey wrote:
On Thu, Oct 22, 2009 at 9:53 AM, S hv sola...@hotmail.com wrote:
Hi,
I am currently working with peptide/lipids
On Oct 22, 2009, at 11:54 AM, albita...@virgilio.it wrote:
Hi,
I'm checking my system and topology but I noticed a quite weird
behaviour in
this concern.
When I run my simulation starting from a pre-optimized geometry, the
simulation
crashes with segmentation fault.
what do you mean by
The type of system you are simulating and the manner you prepared
are probably responsible for the crash ...
You should have a good look at it!
On Oct 19, 2009, at 3:29 PM, albita...@virgilio.it wrote:
Hi all,
I carried out a MD simulation using the MARTINI CG force field and I
had some
I had a look at the notes ... nothing there to satisfy my concerns :))
If gmx-403 is fine on the basic MD level it is then good news.
If anybody recalls some thing I would appreciate to be informed.
Best,
XAvier.
XAvier Periole wrote:
Dears,
I recall the report of a major issue in gmx
I want to calculate the non-bond interaction (LJ+Coulomb) between
solvent and solvent in pure solvent system.
After the simulation of my pure solvent system, I calculated the
interaction between solvent and solvent using the rerun option of
the mdrun program.
First, I set the energygrps
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.
On Sep 9, 2009, at 6:01 PM, Li Yang wrote:
Dear GMXers:
I'm sorry to disturb you.
I have a question about the Marrink's coarse-grained model, Marrink,
et al. Coarse Grained Model for Semiquantitative Lipid Simulations.
J. Phys. Chem. B 2004, 108, 750-760.
First of all you should
On Sep 6, 2009, at 5:39 PM, Ragnarok sdf wrote:
I didn´t actually understand what you meant by, it might be
questionable in regard to its relevance. Is that regarding the
restraint in the Z axis? Would you consider a more correct
protocol to slow down even more the pull rate and hope that
On Sep 5, 2009, at 7:42 AM, Ragnarok sdf wrote:
Hi
I am trying to calculate the PMF by pulling two membrane protein
monomers apart using the pull code with umbrella sampling. While
trying to generate my reaction path, no matter how slow I pull, my
helix starts bending (not really
I am not sure how to fix the trajectory that has drifted ...
But if your bilayer drifts even if you use a removal of the COM for
the water and
bilayer separately that means there is problem in the code! And this
should be
fixed.
XAvier.
On Sep 2, 2009, at 3:36 PM, maria goranovic wrote:
your second value for tau_p is missing the . is this a typo?
On Sep 2, 2009, at 4:45 PM, maria goranovic wrote:
Here are the mdp parameters:
title= POPC
cpp = /usr/bin/cpp
integrator = md
tinit= 0.0
dt
On Aug 27, 2009, at 2:51 PM, sunny mishra wrote:
Dear all,
I was earlier facing problem regarding the mismatch of atoms in .top
and .gro file and then after useful discussion here I figured out
that some atoms were missing in my cg.pdb file and that problem is
because of the OLDER
On Aug 13, 2009, at 21:24, Carla Chiodi carla.chi...@gmail.com wrote:
Hi
Is it possible to simulate the Protein Domain Motion by MD ?
Thank you
Lin
You can do a Coarse-Grained MD using Martini forcefield. You can see
huge domain motions on your protein.
Does not mean it is right!
Hi Johnny,
I am not familiar with pulling and even less with gromacs but I would be
very cautious in using the MARTINI force field for the kind of
simulation
you are doing.
This CG model has not been tested at all for this and it might not be
very good at it! But I would be very interested
On Jul 30, 2009, at 11:40 AM, David van der Spoel wrote:
Marc Baaden wrote:
Hi Xavier (and Johnny),
I quite agree with what Xavier says. Still I would like to point out
that we have used CG models to pull on them and at least
qualitatively
they behave quite reasonably, although these
On Jul 30, 2009, at 12:10 PM, David van der Spoel wrote:
XAvier Periole wrote:
On Jul 30, 2009, at 11:40 AM, David van der Spoel wrote:
Marc Baaden wrote:
Hi Xavier (and Johnny),
I quite agree with what Xavier says. Still I would like to point
out
that we have used CG models to pull
Is it posible to calculate the energy of a protein without to
execute any steps of MD ? I need to claculate the initla enregy but
wihtout excute stesp of dynamic.
How do I fix all atoms of a protein in Gromacs ?
Hasn't that been answered a few days ago!?
just run a zero step md simulation.
On Jul 28, 2009, at 9:50 AM, Morteza Khabiri wrote:
Dear gmx-users,
I am trying to create a tpr file using grompp. My system has a
protein with
four identical chains, 288 POPC molecules, SOL, and ions. I am
trying to
restrain the lipid molecules. When running grompp, I get the
what is not working exactly?
This should give you as output all the pair interacts and you can
select the ones you want ... ?!
On Jul 17, 2009, at 4:23 PM, Ragnarok sdf wrote:
I have created an mdp file with 202 groups for monitoring in the
energygrps string. Being 201 of these aminoacids
I'm trying a coarse-grained simulation with three beads
representing the backbone structure of each residue. However, it's
difficult to get the LJ parameters for -NH- and -CO- . Could anyone
possibly know some work on this?
Well, there is no magic parameters for NH or CO for a
you may want to have a look at the cutoff used by the force field you
defined your
molecule in! 0.5 is definitely too small.
did you minimized?
if your starting configuration does not correspond to the topology,
the use of position
restrains (-DPOSRES) if you actually define them will be
you could use position restrains on the other atoms (non hydrogens) or
use freezing groups.
it seems that your system has a major problem: bad contacts ... check
it prior to EM.
On Jul 6, 2009, at 8:30 AM, nitu sharma wrote:
Dear all
I have to apply only Hydrogen molecule will be
No.
On Jul 6, 2009, at 20:58, Chih-Ying Lin chihying2...@gmail.com wrote:
Hi
In the .mdp file, i set lincs-warnangle = 30.
Will the dihedral angles be affected?
Will the maximum, possible values of the dihedral angles be reduced
because of the setup of the bond constraints?
Thank you
Lin
1. Update to gromacs 4.0.5
2. Your file K.Itp contains repeated instructions
that it should not and therefore the error message.
Build one new from the ions.itp.
I am surprised gromos dos not have K+ ion!
On Jul 6, 2009, at 23:52, sadhna joshi sadhna.jo...@gmail.com wrote:
hi,
I am using
I tried Martini force field and found it calculates with a good
result in appearance
for a *specific* calculation prepared at the Martini website.
That is good to know :))
Now, I wish to use another small molecule (such as lipid) for CG
simulation.
Starting from the chemical structure, I
What is the problem exactly? The two layers separate over the pbc?
did you try a -pbc nojump prior the centering?
On Jul 3, 2009, at 11:37 AM, maria goranovic wrote:
Dear All,
This has been discussed before for individual frames. But I am
having a problem in trying to center a trajectory
at the center of the box (XAvier Periole)
--
Message: 1
Date: Fri, 3 Jul 2009 11:43:55 +0200
From: XAvier Periole x.peri...@rug.nl
Subject: Re: [gmx-users] how to center a MARTINI trajectory so that
the lipid bilayer
Kass)
4. Re: how to center a MARTINI trajectory so that thelipid
bilayer remains at the center of the box (XAvier Periole)
(maria goranovic)
5. Re: Re: how to center a MARTINI trajectory so that thelipid
bilayer remains at the center of the box (XAvier Periole
I would first check that the COM motion ... before reruning! You might
endup
with the same problem if this is not the issue!
On Jul 3, 2009, at 3:26 PM, maria goranovic wrote:
Well .. I will rerun the simulations. setting this would do it, right:
comm_grps = POPC Solvent
where popc and
It seems that your are fine for the energies but the properties
mentioned will be wrong.
On Jun 30, 2009, at 4:48 AM, Jinyao Wang wrote:
hi,gmx-users，
I want to calculate the interaction energy between two group.
So I modify the .mdp file as follows:
energygrps = Protein sol
and make
I looked at one point. The only MD paper using Chlorophyll I found was
Spezia et al Biophys J. 2003, 84:2805-13
On Jun 30, 2009, at 4:49 PM, Julien Maupetit wrote:
Dear all,
I'm trying to evaluate the stability of a (bacterio)-chlorophyll
docked into my protein active site, but it appears
You are right. With MARTINI you often need an rdd bigger than default.
1.4 is reasonable.
On Jun 29, 2009, at 19:33, Michael Lerner mglerner+grom...@gmail.com
wrote:
Hi,
I have a 72-lipid DPPC (MARTINI) system that I ran for 400ns in
GROMACS 3.3.3. I picked a snapshot from the middle
On Jun 20, 2009, at 15:30, Ms. Aswathy S aswat...@amritapuri.amrita.edu
wrote:
using the g_confrm command the RMSD of the protein is 0 (Root mean
square deviation after lsq fit = 4.14581e-08). It means the
structure doesn't have a major change ultimately.. Please correct me
if I am
On Jun 18, 2009, at 11:57 PM, Chih-Ying Lin wrote:
Hi
Here is my whole md.mdp.
But the final Temp = 303 K
No matter I extend the simulation time, the final Temp = 303 K and it
can not reach the ref_t = 300 K
Does it make sense?
Yes unfortunately the 303 K is what you should expect. This is
did you try the option -nojump in trjconv ?
On Jun 19, 2009, at 3:56 AM, Chih-Ying Lin wrote:
Hi
I have a protein+several ligand in the simulation box.
After 5ns, the protein drift to the right edge of the box and the
ligand drift to the left edge of the box.
with this command =
trjconv -pbc
It is simply that if the system is not neutral the Ewald equation are
not valid anymore. I would guess that the original papers describe it.
I never looked into it.
On Jun 19, 2009, at 21:02, Florian Dommert domm...@icp.uni-
stuttgart.de wrote:
* Mark Abraham mark.abra...@anu.edu.au
On Jun 12, 2009, at 4:27 AM, lammps lammps wrote:
When I use CG martini force field to do simulation, and use the
example of Martini website.
There are many warnings when grompp the mdp file:
--
WARNING 4 [file mem16.top, line 41]:
For proper thermostat integration tau_t (0.1)
Dears,
I am having troubles finding the better balance between the PME CPUs
and the rest.
I played with the rdd, rcon and -npme options but nothing really
appears very
straightforwardly best.
I'd appreciate if some of you could post their experience in that
matter. I mean the
number of
On Jun 6, 2009, at 1:08 PM, Justin A. Lemkul wrote:
XAvier Periole wrote:
Dears,
I am having troubles finding the better balance between the PME
CPUs and the rest.
I played with the rdd, rcon and -npme options but nothing really
appears very
straightforwardly best.
I'd appreciate
On Jun 4, 2009, at 4:18 PM, Sarah Witzke wrote:
Dear gromacs users,
I have done several simulations with small lipophilic, molecules
diffusing into a DMPC bilayer.
I would like to calculate the diffusion coefficient of the molecules
inside the membrane, and therefore I looked at
-5 ; 1/bar (water @ 1 atm, 300 K)
ref_p = 1.0 1.0 ; bar
#
Fra: gmx-users-boun...@gromacs.org på vegne af XAvier Periole
Sendt: fr 05-06-2009 09:34
Til: Discussion list for GROMACS users
Emne: Re: [gmx
On Jun 4, 2009, at 10:10 AM, subarna thakur wrote:
hello everyone
Can any body please explain to me, what does the trm gb_38 or gb_39
stand for under the bond coulmn of the ..rtp file ? what is gromos
type under angles and impropers?
gb_XX stands for the XX type of gromos bond, ga_XX for
Dears,
I am experiencing some problems running a few proteins in water
(GROMOS43a1/SPC)
with gmx-4.0.4 using 32 CPUs.
After some ns lincs warnings appear and eventually the simulation
crashes dues
to too many lincs warnings.
When restarting the simulation feeding -cpi md.cpt to mdrun
On Jun 3, 2009, at 9:51 AM, Mark Abraham wrote:
XAvier Periole wrote:
Dears,
I am experiencing some problems running a few proteins in water
(GROMOS43a1/SPC)
with gmx-4.0.4 using 32 CPUs.
After some ns lincs warnings appear and eventually the simulation
crashes dues
to too many lincs
would have considered this if the warning were reproduced when
restarting the simulation.
It seems more that it is a loss of accuracy due to communication
between CPUs ?
XAvier.
Ran.
XAvier Periole wrote:
Dears,
I am experiencing some problems running a few proteins in water
(GROMOS43a1/SPC
, or enlarge the
solvation cell.
Thanks, I have however a very large water box and no problem there I
believe.
Hope this helps,
Giovanni
On Wed, Jun 3, 2009 at 10:48 AM, Erik Marklund
er...@xray.bmc.uu.se wrote:
XAvier Periole skrev:
On Jun 3, 2009, at 10:01 AM, Ran Friedman wrote:
Hi
On Jun 3, 2009, at 10:48 AM, Erik Marklund wrote:
XAvier Periole skrev:
On Jun 3, 2009, at 10:01 AM, Ran Friedman wrote:
Hi XAvier,
Do you use virtual sites? I've seen this when I used virtual sites,
No virtual sites.
large time steps and a system that probably wasn't equilibrated
You should have a look at the manual/wiki/online documentation.
You'll find everything you need.
On Jun 3, 2009, at 8:28 PM, rituraj purohit wrote:
Hello to everybody
I need the gromacs analysis document. I mean i want to do analysis
(like; RMSD, traj)of my result which I got after
On Jun 1, 2009, at 1:12 PM, Stefano Meliga wrote:
Hi again,
The energy minimization with conjugate gradient integrator still
gives me two warnings of the type:
t = 0.011 ps: Water molecule starting at atom 28122 can not be
settled.
Check for bad contacts and/or reduce the timestep.
My
Don't know about the missing interactions ... never seen this in any
of the
gmx versions using Martini ...
for the error you should increase the -rdd to 1.4/1.5 nm
On May 13, 2009, at 4:36 PM, maria goranovic wrote:
Dear All,
I ran a POPC simuIation in gromacs 3.3.1 with the martini
On May 11, 2009, at 6:18 AM, Chih-Ying Lin wrote:
Hi
GROMOS 45a3 force field
GROMOS 53a6 force field
Are they compatible?
Probably not. They are two different parameterization generations.
The 53a6 being more recent! Mixing them is probably not a good idea!
They have been parameterized
On May 9, 2009, at 12:50 PM, David van der Spoel wrote:
David van der Spoel wrote:
XAvier Periole wrote:
Dears,
I am asking for the angular removal of the COM motion of a protein
assembly
in gromacs-4.0.4.
- grompp gives a strange warning:
checking input for internal consistency
On May 9, 2009, at 12:50 PM, David van der Spoel wrote:
David van der Spoel wrote:
XAvier Periole wrote:
Dears,
I am asking for the angular removal of the COM motion of a protein
assembly
in gromacs-4.0.4.
- grompp gives a strange warning:
checking input for internal consistency
Dear Dennis,
I believe your problem is due to the fact that when the
autocorrelation is
done on a dihedral angle a cos function is used instead of the angle
itself.
This is good to account for periodicity. This function is not
implemented
in the -P 1 2 3 ... if I recall correctly.
I
-
XAvier Periole - PhD
- Molecular Dynamics Group -
Computation and NMR
University of Groningen
The Netherlands
-
___
gmx-users mailing listgmx-users@gromacs.org
you have the choice of using the -dt XX option of g_hbond which will
tell to analyze only every XX structure. I am not sure this is present
in
g_hbond.
the other way is to use trjconv with the dt option again an write the
frames every XX steps.
On Apr 21, 2009, at 9:26 PM, Aaron Fafarman
You may have defined position restraints that exceed the number of atoms
present your system, or define them in a wrong manner.
Check manual and previous posts.
On Apr 15, 2009, at 12:29 AM, Justin A. Lemkul wrote:
He, Yang wrote:
HI Justin,
I just use the mdrun command and then get such
It is probably best to fix your lipid bilayer problem first. Inserting
a protein won't fix the problem(s).
XAvier
On Mar 31, 2009, at 8:05, nitu sharma sharmanit...@gmail.com wrote:
Dear all,
I am trying to simulation of membrane proteins I
have a basic question can
It is a bit difficult to guess what is exactly happening. Your
starting structure
seem to be the problem, but your topology could also be partly
responsible.
One easy thing to do is the decrease your time step to 0.0001 which
would
decrease the chances that your system explodes.
Also
.
Another option (in addition to doing the background reading!) is to
run through some tutorial material with a simple protein under OPLS
to get a feel for how an OPLS topology is automatically created by
pdb2gmx.
-Justin
Thank you again.
Sincerely,
Kim
On Mon, Mar 16, 2009 at 5:42 PM, XAvier
You've probably conflicts of restrains and forces in your system.
Note that our definition of the position restraints if applicable to
all solvent molecules should be :
[position_restraints]
1 1 0 0 1000
2 1 0 0 1000
3 1 0 0 1000
if not it will look at the atom of the solvent number 34083 ...
On Mar 16, 2009, at 9:34 AM, tree wrote:
Dear Justin and All:
I truly appreciate your clear answer.
Since my questions are solved by your explanations, I do not know
how I can express my grateful heart.
Now I have to ask second step questions. :)
It is related to the OPLS-aa bon.itp
an idea? may be Berk?
Thanks,
XAvier.
XAvier Periole
MD-Group / Groningen
The Netherlands.
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On Mar 16, 2009, at 5:51 PM, Antonia V. wrote:
Hello,
I am wondering if there is a tool implemented in GROMACS that
computes the
coordinates of the center of mass of each molecule of a simulation
box.
g_traj -f traj.xtc -com
Thank you
Antonia
Invite your mail contacts to join your
mdrun complains when I am asking for the angular removal of the COM
together
with dynamic load balance on (with gmx-4.0.4). It says the
combination
You mean domain decomposition.
Yes, sorry!
By imposed I mean that the flags are explicitly changed to do angular
removal of
COM (remove
Indeed we are lucky then!
In the mean field there no periodic boundary, the system is spherical.
Thanks.
XAvier.
On Mar 16, 2009, at 7:05 PM, Berk Hess wrote:
Hi,
I think you are lucky.
The angular comm code only does not work with DD when molecules are
partially over the periodic
Hi Rodney,
the other alternative is to define the springs in your topology file.
You first need to merge
your groups (is part of different molecules) and run the different
combination you need by
defining them by hand; you can easily write a awk script to generate
the different topologies
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