Hello everyone,
I'm computing the relative binding free energies of DNA bases on a
nanotube using the protocol listed here:
http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial
I'm using the following steps:
1. Turn off all charges on base
2. Transform LJ parameters
3. Turn on a
Hello everyone,
When performing a relative binding free energy calculation, I
understand that it is a good practice to separate the transformation
of charges of the ligand and the transformation of vdW parameters into
two calculations. However, is it advisable to completely discharge the
ligand bef
Hello everyone,
I'm using Gromacs 3.3.3 and I'm trying to equilibrate the solvent
around a protein. At first I am freezing the C-alphas and restraining
the rest of the protein. The waters are free to move. However, when I
use these freeze groups, the simulation results in the box/solvent
exploding.
Hello everyone,
Sorry if you get this twice. It seems to me that the previous message
didn't go through.
I'm computing the binding free energy of DNA bases (just the base, no
sugar, no phosphate) on a carbon
nanotube following the prescirption of the Dill group Wiki
(http://www.dillgroup.ucsf.edu
Hello everyone,
I'm calculating the relative free energy of binding of DNA bases on a
carbon nanotube via thermodynamic integration. Because I'm interested
in the relative binding free energies, I'm morphing G into A followed
by A into C and so on.
My question is, is there a way to extract the rel
Dear Colleague.
We cordially invite you to register for the:
3rd Annual CMM 'Users Meet Developers' Workshop on QM/MM Simulations
August 21st to 23rd 2008 in Philadelphia, PA
* Goals
The primary goal of this annual workshop is to encourage communication between
users and developers of
Well, the end caps contain a few pentagons so the angle terms for
those atoms would have to change from the normal 120 degrees used for
hexagons. Other than that, I don't think the force field parameters
would have to change. What do you mean by the tube "breaking apart"?
That sounds like you don't
; Perhaps a naive question, but which version of Gromacs are you using? Such
> issues are well-known in 3.3.1, but have been fixed in the most recent release
> (3.3.3).
>
> -Justin
>
> Quoting Robert Johnson <[EMAIL PROTECTED]>:
>
>> Hi Maik,
>> That's
te, Dipl. Biol.
> Max Planck Institute for Biophysical Chemistry
> Theoretical & computational biophysics department
> Am Fassberg 11
> 37077 Goettingen
> Germany
> Tel. : ++49 551 201 2310
> Fax : ++49 551 201 2302
> Email : mgoette[at]mpi-bpc.mpg.de
> mg
Hi David,
Yes...sorry...I'm doing a 7.5 ns for each lambda value (lambda = 0,
0.25, 0.5, 0.75, 1.0). Every single simulation takes place from the
exact some starting configuration. No restraints are being used. The
calculation I'm planning on doing (once everything is worked out) is a
relative bind
Hello everyone,
I'm trying to calculate the free energy of binding of DNA bases on a
carbon nanotube. I'm running some tests to make sure that I'm doing
everything correctly. One thing I tried was turning off all the atom
charges of the DNA base and then turning them back on again.
Theoretically, t
Hello Pascal,
I'm not sure I can really comment on (1), but the reason why your
energy gap decreases in (2) is because the energy fluctuations in your
system increase as you raise the temperature. For example, at low
temperatures your potential energy distributions will be sharply
peaked about the
Hello everyone,
I posted this question a week ago and no one commented on it. I would
appreciate it if someone could answer this. I would like to compute
the free energy of turning on orientation restraints (1 distance, 2
angle, 3 dihedral). I'm using Gromacs v. 3.3.1 and there doesn't seem
to be a
Hello everyone,
I would like to compute the free energy of turning on orientation
restraints (1 distance, 2 angle, 3 dihedral). I'm using Gromacs v.
3.3.1 and there doesn't seem to be a way to perturb the dihedral
restraints section of the topology file. Has this feature been
implemented in v. 3.3.
Thanks for your response David.
Are you assuming that the lambda dependence of the restraint follows
from equation 4.113? Or do you use the expression in equation 4.100
for harmonic potentials? If the latter, I'm unsure how to apply this
equation for the dihedral restraints (equation 4.70) - agai
Hello everyone,
I'm computing the free energy of binding between a DNA base and a
carbon nanotube. I'm following the recipe given in Boresch et. al. J.
Phys. Chem. B. 107, 2003 where the ligand (the base in my case) is
restrained. The free energy of turning on the restraints is included
in the over
side the allowed range back into that allowed range.
>
> David
>
>
> On Mon, Feb 25, 2008 at 2:24 PM, Robert Johnson
>
>
> <[EMAIL PROTECTED]> wrote:
> > Well, the potential is of the form V=k(x1-x2)^2, but I don't see how
> > it's harmonic.
that correct?
Thanks,
Bob
On Tue, Feb 26, 2008 at 1:15 AM, Mark Abraham <[EMAIL PROTECTED]> wrote:
> Robert Johnson wrote:
> > Well, the potential is of the form V=k(x1-x2)^2, but I don't see how
> > it's harmonic. What you would want is the x1 and x2 to refer t
ing at, but in the GROMACS 3.3
> manual, equation 4.70 gives the dihedral restraint as harmonic.
>
> David
>
>
>
>
> On Mon, Feb 25, 2008 at 10:10 AM, Robert Johnson
> <[EMAIL PROTECTED]> wrote:
> > Hello everyone,
> > I am trying to calculate the
Hello everyone,
I am trying to calculate the absolute free energy of binding between a
DNA base and a nanotube. To do this, I am first calculating the free
energy associated with restraining the base in the correct binding
geometry in accordance with Boresch et. al. J. Phs. Chem. B., 107,
2003. In
t; Tel. : ++49 551 201 2310
> Fax : ++49 551 201 2302
> Email : mgoette[at]mpi-bpc.mpg.de
> mgoette2[at]gwdg.de
> WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
>
>
> Robert Johnson wrote:
> > Thanks David,
> > Since I'm turning off the VdW parameter
ey <[EMAIL PROTECTED]> wrote:
> It will only be smooth if you don't use soft core (i.e. sc-alpha =0 ).
>
> Best,
> David Mobley
> http://www.dillgroup.ucsf.edu/~dmobley
>
>
> On Jan 25, 2008 12:40 PM, Robert Johnson <[EMAIL PROTECTED]> wrote:
> > Hello every
Hello everyone,
As I mentioned in a previous post, I'm trying to compute the free
energy of binding of a DNA base on a carbon nanotube. My system
consists of a single DNA nucleotide (base, sugar, phosphate group) on
a rigid carbon nanotube in aqueous solution. A single Na+ counterion
is also includ
ysics department
> Am Fassberg 11
> 37077 Goettingen
> Germany
> Tel. : ++49 551 201 2310
> Fax : ++49 551 201 2302
> Email : mgoette[at]mpi-bpc.mpg.de
> mgoette2[at]gwdg.de
> WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
>
>
> Robert Johnson wrote:
>
1 201 2310
> Fax : ++49 551 201 2302
> Email : mgoette[at]mpi-bpc.mpg.de
> mgoette2[at]gwdg.de
> WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
>
>
> Robert Johnson wrote:
>
> > Thank you David and Maik for your detailed replies. Yes, I am trying
> >
Thank you David and Maik for your detailed replies. Yes, I am trying
to obtain an absolute free energy of binding. My thermodynamic cycle
is:
NT+DNA(adsorbed) -> NT+ DNA(desorbed) (obviously this is not the one
that I'm obtaining with the alchemic method)
Thus, the one I'm using in the simulatio
Hello everyone,
I'm computing the free energy of binding of a DNA base on a carbon
nanotube. I think it's a pretty simple calculation and I'm proceeding
in a very standard way. This is what I'm doing:
I have the optimal orientation of the base on the nanotube. I'm
constraining the positions of the
Hi Joshua,
Since each carbon-carbon bond is identical, you can just include the
bonded information as a separate .itp file or at the top of your
system .top file. For example, at the top of your .top file you can
include the [ defaults ], [ atomtypes ], [ bondtypes ], [angletypes],
[dihedraltypes],
Are you absolutely sure that the terminal carbon atoms are sharing a
bond in the topology file? Make sure of this. If they really ARE
bonded within the topology file, then I don't think the crumpling is
due to Gromacs incorrectly reading the topology (by the way, use
pbc=full). Provided that the to
Hello everyone,
I'm performing PCA on single stranded DNA adsorbed to a carbon
nanotube which is aligned along the z-axis. Because the DNA is
adsorbed, fitting each frame to the average structure via a 3D
translation and rotation doesn't make sense. In my analysis, I
minimize the RMSD between each
Can anyone recommend a remedy/explanation for this?
Thanks,
Bob
On 9/19/07, Robert Johnson <[EMAIL PROTECTED]> wrote:
> Hello everyone,
> Eventually I want to pull a carbon nanotube through water at a
> constant rate. Before I get to this, I'm pulling a nanotube in vacuum
>
Hello everyone,
Eventually I want to pull a carbon nanotube through water at a
constant rate. Before I get to this, I'm pulling a nanotube in vacuum
just to make sure I'm using the pull code correctly.
My system consists of a carbon nanotube aligned along the z axis and a
single dummy atom fixed o
Think about what a carbon nanotube isyou can think about it as a
rolled up graphene sheet. Graphene is made up entirely of sp2 carbons
- which means that the carbons want to reside in a planar arrangement.
Rolling the sheet up into a tube requires energy. Your positive energy
reflects this.
Bob
You can check out the Gromacs Wiki pages:
http://wiki.gromacs.org/index.php/Development
http://wiki.gromacs.org/index.php/CVS_HowTo
Bob
On 8/29/07, Arturas Ziemys <[EMAIL PROTECTED]> wrote:
>
> How to access CVS of GROMACS ?
>
> Robert Johnson wrote:
> > The CVS version
The CVS version of Gromacs enables REMD simulations where each replica
can be run across multiple CPUs.
Bob
On 8/29/07, Arturas Ziemys <[EMAIL PROTECTED]> wrote:
> Hi,
>
> After I was reading manual on REMD and mdrun, I understood that GROMACX
> is capable to run REMD using just one node per repli
The best and easiest way to do this would be to write a script within
VMD. You can define an atom selection something like:
set wat_inside [atomselect $mol_id "same residue as water and (z >
$NT_beg and z < $NT_end and sqrt((x-$x_NT)*(x-$x_NT) +
(y-$y_NT)*(y-$y_NT)) < $NT_radius)]
Here $mol_id is
hint or ref.
> >> >
> >> > Thanks so much,
> >> >
> >> > ~Christopher Stiles
> >> > College of Nanoscale Science and Engineering (CNSE)
> >> > State University of New York, Albany, New York 12203, USA
> >> >
>
; any one knows already knows please feel free to give me a hint or ref.
> >
> > Thanks so much,
> >
> > ~Christopher Stiles
> > College of Nanoscale Science and Engineering (CNSE)
> > State University of New York, Albany, New York 12203, USA
> >
> >
Did you define angle and dihedral parameters in the [ angletypes ] and
[ dihedraltypes ] sections of your .itp file?
Bob
On 7/27/07, Christopher Stiles <[EMAIL PROTECTED]> wrote:
> The warnings are:
> ...
> WARNING 701 [file "SWNT_6_6_144.top", line 1278]:
> No default Angle types, using zeroes
Hi Chris,
Yes, the bondtypes, etc. sections go in the .itp file.
The only way (I know of) to respond to a specific thread is to have an
email from that thread.
Bob
On 7/26/07, Christopher Stiles <[EMAIL PROTECTED]> wrote:
> Yang,
> Thank you again for being so detailed. I do have 2 questi
Hi Chris,
You will have to pick the force field you want to use and include that
information after you generate the topology file. You can leave out
the force field parameters in your topology file. You can then add
these parameters in [ bondtypes ], [ angletypes ] and [ dihedraltypes
] sections (
Hi Chris,
Can you visualize your nanotube coordinates with a program like VMD to
make sure that it looks ok? However, I'd assume your coordinate file
is just fine.
First off, do you want to simulate a finite nanotube or an infinite nanotube?
If you want an infinite nanotube do this:
1) Orient na
Hello everyone,
I asked this question in the past without a response, so I'll give it
another shot.
There have been other reports on the mailing list where users attempt
to generate
a topology with x2top only to have the program stall and generate no output. I'm
using x2top (from Gromacs version
ig problem - make of it what you will. ;-)
Bob
On 6/13/07, Erik Lindahl <[EMAIL PROTECTED]> wrote:
Hi Robert,
On Jun 13, 2007, at 6:48 PM, Robert Johnson wrote:
> These are all fine points. However, the question I'm asking is why do
> Gromacs tools change atoms named OXT in
esday, June 12, 2007 15:30 -0400 Robert Johnson
<[EMAIL PROTECTED]> wrote:
> Hello everyone,
> I'm attempting to run a simulation of a protein that contains an atom
> named OXT (for the terminal oxygen atom). We are using the amber force
> field and have already successfull
Hello everyone,
I'm attempting to run a simulation of a protein that contains an atom
named OXT (for the terminal oxygen atom). We are using the amber force
field and have already successfully built a topology for the protein.
However, when running Grompp we consistently receive the following
erro
Use anything with sp2 carbon parameters. There are a bunch of
different sp2 atom types, however they all have the same lennard-jones
parameters.
Bob
On 6/4/07, bo yang <[EMAIL PROTECTED]> wrote:
Dear gromacs user,
I am doing a CNT-water simulation with using ffamber99 forcefield.
I don't know
Just take the coordinate files for the protein and the nanotube, cat
them together and then edit the resulting file. Then you can solvate
the composite system using genbox.
Bob
On 5/10/07, George Abadir <[EMAIL PROTECTED]> wrote:
Hi,
I have built a topology file for a protein and a topolgy
Hi Dhanajay,
Since you don't have a trajectory (yet) and are comparing different
structures, I think the easiest thing to do would be to compute this
with VMD (www.ks.uiuc.edu/Research/vmd). You would load your PDB files
in separately, go to the TK console and type:
set struct1 [atomselect "all"
Send an email to [EMAIL PROTECTED]
On 4/19/07, yuemin liu <[EMAIL PROTECTED]> wrote:
That is very interesting. I once did QM/MM with
Gaussian and am thinking of using gromacs.
How can I register?
Thanks,
--- Robert Johnson <[EMAIL PROTECTED]> wrote:
> Dear Colleague.
>
>
Dear Colleague.
We cordially invite you to register for attending the:
2nd CMM 'Users Meet Developers'
Workshop on QM/MM Simulations
August 24th to 26th in Philadelphia, PA
* Goals
The primary goals of this workshop are to encourage communication
between different QM/MM approaches and
Do you want to simulate an infinite nanotube or a finite one?
Bob
On 3/28/07, George Abadir <[EMAIL PROTECTED]> wrote:
There is no C1 and C2 atom in the input PDB file, and the topology file
is not generated because x2top doesn't generate a topology because of
the errors. I don't understand what
When using x2top with a specific force field, things are assumed about
the connectivity of the molecule. The terminal carbon atoms of your NT
will only be bonded to, at most, 2 other carbons. In your case, it
looks like they are only bonded to one. When x2top tries to find the
forcefield associate
You could write your own program or script to do it. If you are
interested in zigzag or armchair nanotubes, this is pretty trivial to
do. Otherwise, Tubegen should be fine.
Bob
On 3/27/07, George Abadir <[EMAIL PROTECTED]> wrote:
Hi,
I am using Tubegen to generate carbon nanotubes for my si
Hello everyone,
I'm performing a simulation that includes a 2D infinite SiO2
substrate. I'm not interested in the high frequency motion of the
substrate bonds, so I'm applying position restraints to all the SiO2
atoms. I have other molecules in the system such as water and DNA that
require hydroge
If they are at the carbon-carbon bond distance, then their van der
Waals radii will be overlapping and the force between them is huge.
You can turn off this interaction with energygrp_excl = atom1 atom2
(with atom1 and atom2 defined in your index file).
I'm not sure why your atoms would be moving
Maybe this is a stupid suggestions butdid you check if your two
atoms are centered in the box and that the box dimensions are big
enough to accomodate your system? Maybe the atoms appear to be "flying
apart" because periodic boundary conditions are being applied.
Bob
On 3/16/07, David Mobley
Hello everyone,
As I was discussing in a previous thread, I'm having problems
visualizing/analyzing an REMD trajectory of ssDNA. As I understand,
most tools for unwrapping PBC (i.e. removing the jumps from one side
of the box to the other) do so by detecting large displacements
between successive
n A in the center would mean that there's a periodic image
> of your chain B which has its first atom in the center. This image
> will be chosen during the generation of the .tpr file. Converting the
> .tpr to .pdb should give both chains close to each other. Processing
> the trajector
k Wassenaar wrote:
> Hi Bob,
>
> You could try -pbc cluster. If that doesn't work, it'll be difficult.
> The option -pbc nojump will only work on continuous trajectories.
>
> Cheers,
>
> Tsjerk
>
> On 3/14/07, Robert Johnson <[EMAIL PROTECTED]> wrote:
>&
Hello everyone,
I'm trying to visualze the conformations of a ssDNA molecule obtained from a
REMD trajectory. As expected, there are parts of the simulation where the
oligomer is broken due to the PBC wrapping. I've been trying to fix this with
trjconv. However, the -pbc nojump option doesn't work
So, does g_traj really give you a trajectory that has the COM velocity
of the droplet removed? It looks like this is what you were trying to
do, but I just wanted to be clear on the outcome.
If that is the case you can do an mdrun -rerun no-com-traj.trr. This
will feed your COM removed trajectory
If you wanted to study a collision, why do it at constant temperature?
Like David said, maybe you should equilibrate the droplet at 300K, add
a center of mass velocity to the droplet, and then study the collision
at constant energy. The real collision probably doesn't take place at
constant temper
Use semiisotropic pressure coupling with with the compressibility and
reference pressure both 0 in the xy dimension.
Bob
On 2/15/07, toma0052 <[EMAIL PROTECTED]> wrote:
Hello,
I am looking to do a membrane simulation where I have a constant
pressure normal to the membrane, and a fixed area
Will function type 5 or 6 (for the harmonic bond) affect the
non-bonded exclusion list?
On 2/3/07, Mark Abraham <[EMAIL PROTECTED]> wrote:
Robert Johnson wrote:
> You can apply a harmonic bond between the two atoms.
More precisely, you should apply harmonic distance restraints.
You can apply a harmonic bond between the two atoms.
On 2/3/07, Srinivas Ramachandran <[EMAIL PROTECTED]> wrote:
Dear all,
I know that we can place harmonic constraints on selective atoms,
specified by an index file. But this only ensures that the atom
position remains same throughout the simul
Hello everyone,
I'm new to Principle Components Analysis, so correct me if I'm wrong.
If you have a collection of protein structures from a replica exchange
calculation, for example, I believe you can reconstruct each of them
from its average structure by the following:
r(t) = + p_1(t) v_1 + p2(
gt;
> for($k=0; ($k<$nrepl); $k++) {
>$order[$k] = $k;
>$revorder[$k] = $k;
> }
>
>To read in the data in the last line of the previous replica_index.xvg and
>replica_temp.xvg.
>
>Regards,
>Yang Ye
>
>On 1/27/2007 5:05 AM, Robert Johnso
Hello everyone,
I'm currently running REMD and using the demux.pl script provided by
David to generate replica_index.xvg and replica_temp.xvg files. I
noticed that each time you restart the simulation (e.g. to extend the
trajectory), all information about the replica index number is lost
and the r
I think you are getting that error about NaN because you have water
molecules that are almost exactly on top of one another.
If you just want a box of water, the easiest way to do it is this:
genbox -cs -o water.pdb -box
Here, x y and z are the box dimensions in nanometers. You can play
with
Hi Marc,
Yes, I get the same Segfault. The way I have calculated bonded energy
terms for subsets is to just copy the topology file and then comment
out the unwanted terms.
Bob
On 1/22/07, Marc Baaden <[EMAIL PROTECTED]> wrote:
>>> David van der Spoel said:
>> > Just to make sure I get this ri
Hi Marc,
The only way I know how to do this is to make a copy of the topology
file that ONLY contains the bonded terms that you want. Then use the
mdrun -rerun option to recalculate the bonded energies for those
terms. You must do this because I think that bonded energies are only
written for the
Hello everyone,
I recently ran a replica exchange calculation using the development
version of Gromacs. I used the demux.pl script to generate the two
.xvg files. I am trying to feed the replica_index.xvg file to trjcat,
but I'm getting a strange error message that I don't understand. Here
is the
one every
0.6 ps. There were 64 replicas total and each replica was running on
32 processors.
Also, what will trjcat give me? Will it give trajectories that are at
a constant temperature?
Thanks,
Bob
On 1/16/07, David van der Spoel <[EMAIL PROTECTED]> wrote:
Robert Johnson wrote:
> He
Hello everyone,
I'm using the current development version of Gromacs to perform
replica exchange MD. Are there any Gromacs tools to aid in the
analysis of the trajectories. For example, are there tools that enable
trajectories grouped by temperature? Is there a way to determine the
temperature of
Hello everyone,
I am trying to run some benchmakrs on a replica exchange simulation. I
have several .tpr files: topol0.tpr, topol1.tpr, topol2.tpr, up to
topol7.tpr. I would like the calculation to proceed all on the same
node (for benchmarking and debugging reasons and so I don't have to
wait in
They need to be named remd0.tpr, remd1.tpr, remd2.tpr etc. Then mpirun -n
4 mdrun -np 4 -s remd will do the job. "man mdrun" has the details.
Don't I have to use the -multi and -replex flags somewhere? When I
just give -s remd (i.e. the prefix for the .tpr files), I get an error
message saying
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