Hi Rajat,
If you remove comm on the bilayer, there may be relative comm between
leaflets. If that relative motion is significant and you switch to removing
comm per leaflet, the program suddenly finds itself resetting the com over
a large distance. About equilibration, you equilibrated with
Hi Debashis,
Makes sure that the anion and receptor are together in the reference
structure you use for trjconv -pbc nojump
Cheers,
Tsjerk
On Tue, Nov 5, 2013 at 8:12 AM, Debashis Sahu debashis.sah...@gmail.comwrote:
Dear All,
I have an problem related to jumping trajectory.
Hi Blake,
Centering on the solute should help.
Cheers,
Tsjerk
On Sat, Nov 2, 2013 at 3:55 PM, rankinb rank...@purdue.edu wrote:
Hi all,
I am trying to use trjconv to remove PBC. More specifically, I would like
to extract the coordinates of all the water molecules within a certain
Hi Nahren,
You can try the .g96 format for this, which has high precision. To
understand the format, convert something to .g96 and replace the
coordinates with the eigenvectors.
Hope it helps,
Tsjerk
On Fri, Nov 1, 2013 at 4:10 AM, nahren manuel meetnah...@yahoo.com wrote:
Dear GMX Users,
Hi Musyoka,
I would guess that that is related to the input coordinates. A bit of EM
should fix it.
Cheers,
Tsjerk
On Mon, Oct 28, 2013 at 11:20 AM, MUSYOKA THOMMAS
mutemibiochemis...@gmail.com wrote:
Dear Users,
Whenever i convert a protein.pdb file using the following command (pdb2gmx
Hi Shahab,
What about running trjconv -pbc mol with a .tpr as input file?
Cheers,
Tsjerk
On Sun, Oct 27, 2013 at 3:24 PM, shahab shariati
shahab.shari...@gmail.comwrote:
Dear Justin
I attached images related to before (em2.gro) and after equilibration.
Hi Nidhi,
These are periodicity artifacts. Make sure that you remove jumps over PBC
from your trajectory by using trjconv -pbc nojump.
Cheers,
Tsjerk
On Tue, Oct 22, 2013 at 11:14 AM, Nidhi Katyal nidhikatyal1...@gmail.comwrote:
Dear all users
I have simulated a protein with two chains
Hi :)
Apologies if this seems inappropriate, but I would like to ask as many
people as I can to give support for the molecular modeling LEGO project at
http://lego.cuusoo.com/ideas/view/51273. With 10 000 votes, LEGO will
consider producing the bricks required for such models, and we can add cool
Hi James,
There are models, yes. But if a manufacturer like LEGO is taking this up,
it can make the models much cheaper and more easily available. In addition,
the LEGO models would allow more flexibility in building and handling. And
you can combine it with your other LEGO ;)
And, yes, bendy
Hi DeepaK,
You should be aware that excess protons are not floating around freely
among a bunch of H2O. Whatever reasoning along this line is physically
meaningless (including thinking of a mixture of H3O+, H2O, OH-). This is
the realm of QM.
Cheers,
Tsjerk
On Thu, Oct 10, 2013 at 8:05 AM,
Dear Dwey,
Please direct questions like this to the gromacs user list, after asserting
that the answer has not already been given. In addition, please read
http://md.chem.rug.nl/~mdcourse/molmod2012/md.html
Regards,
Tsjerk
On Tue, Oct 8, 2013 at 5:35 PM, Dwey mpi...@gmail.com wrote:
Dear
Hi Lin,
I would say that it is not correct to call 45a3 deprecated. Like other
force fields, GROMOS 45a3 is also the result of careful parameterization.
The later GROMOS forcefields 53a5, 53a6, 54a7 and 54a8, took of a
completely different approach in parameterization, and are in that respect
not
Hi Prathiba,
I think you should have a look at the Functional Mode Analysis method
from Bert de Groot's lab.
Cheers,
Tsjerk
On Sat, Sep 28, 2013 at 8:13 AM, pratibha kapoor
kapoorpratib...@gmail.comwrote:
Dear all users
I would like to calculate pc loadings for various integrated factors
Yes.
Cheers,
Tsjerk
On Fri, Sep 27, 2013 at 7:51 AM, Venkat Reddy venkat...@gmail.com wrote:
Thanks for the quick reply sir.
So, does it mean I can apply trjcat on the processed xtc files???
On Thu, Sep 26, 2013 at 10:25 PM, Tsjerk Wassenaar tsje...@gmail.com
wrote:
Hi Venkat
Hi Pratibha,
The table is all garbled, and your description insufficiently clear for us
to form a mental picture of what you want, what you've tried to get that,
where it goes wrong, or where you get stuck, and how we can help you on the
right track again.
Cheers,
Tsjerk
On Fri, Sep 27, 2013
Hi Venkat,
It depends on what you mean with removing pbc.
Cheers,
Tsjerk
On Sep 26, 2013 5:21 PM, Venkat Reddy venkat...@gmail.com wrote:
Dear Sir,
Thanks for the quick reply.
I accidentally lost one of my raw .xtc files. But I have the noPBC xtc
file. So, when ever I extend my simulation,
Hi Venkat,
These options are 'frame intrinsic' or 'history independent', unlike -pbc
nojump.
Cheers,
Tsjerk
On Sep 26, 2013 6:46 PM, Venkat Reddy venkat...@gmail.com wrote:
Dear Tsjerk sir,
I used trjconv -pbc mol -ur compact options.
On Thu, Sep 26, 2013 at 9:17 PM, Tsjerk Wassenaar tsje
Hi Kavya,
genconf -nbox 3 3 3
Cheers,
Tsjerk
On Thu, Sep 26, 2013 at 6:24 PM, Kavyashree M hmkv...@gmail.com wrote:
Dear users,
For some analysis I require the 27 periodic images
of the system I ran the simulation for. Kindly let me
know how can it be written to a pdb file.
Thanking
Hi Ángel,
kJ per mol of system contained in the unit cell?
Exactly. As if whatever is in there is one 'molecule' (-nmol 1).
Adios!
Tsjerk
--
Tsjerk A. Wassenaar, Ph.D.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search
It's the size of the attempted step in conformational space, the distance
from one configuration to the next.
Cheers,
Tsjerk
On Sep 21, 2013 10:11 PM, Justin Lemkul jalem...@vt.edu wrote:
On 9/21/13 2:47 PM, Atila Petrosian wrote: Dear Justin Thanks for
your reply. Ok. You ...
A quick
Hi Deniz,
The option -ref/-noref is not what you think it is. You want to use -nofit.
Cheers,
Tsjerk
On Fri, Sep 20, 2013 at 2:26 PM, Deniz Aydin denizay...@ku.edu.tr wrote:
Dear All,
I would like to get information on how g_covar calculates the average
structure file (average.pdb)
My
Hi Shahab,
You edited the .gro file, but you made an error. So you have to read the
manual to understand the file format and then see where and how your edited
file doesn't match.
Cheers,
Tsjerk
On Thu, Sep 19, 2013 at 5:00 PM, shahab shariati
shahab.shari...@gmail.comwrote:
Dear Tsjerk
Hi Shahab,
What did you do exactly? Can you state your complete protocol (1. fetched
this structure file there, 2. got the topology from there, 3. did
something, 4. ran grompp like this, etc)? Use brief, clear explanations and
the command lines as you issued them.
Cheers,
Tsjerk
On Tue, Sep
Hi Shahab,
That site has a lot of structures. It would be better to explicitly state
which one you took. However, in this case, the better question is, how did
you write the topology, and did you check the correspondence of the order
of molecules/atoms in the topology file and the structure file?
Hi Neha,
Yes. The MN* particles are the virtual sites.
Cheers,
Tsjerk
On Wed, Sep 18, 2013 at 7:13 AM, Neha Gandhi n.gandh...@gmail.com wrote:
Dear Users,
I am trying to prepare file using pdb2gmx using Gomos 43a1 ff. I am
using following command.
pdb2gmx -f input.gro -o input1.gro
Hi Santhosh,
Try renaming the atom (mind the space):
sed 's/OXT/O2 /' pdbfile fixed.pdb
And then run pdb2gmx on that.
Cheers,
Tsjerk
On Tue, Sep 17, 2013 at 6:05 AM, Santhosh Kumar Nagarajan
santhoshraja...@gmail.com wrote:
This is the command I used
pdb2gmx -f protein.pdb -o
Hi Dallas, Justin, e.a.,
As has been mentioned a number of times 0.9 +- 190 and 2.3 +- 190 are not
statistically different.
This is not true. Whether this is statistically different depends on the
number of independent samples. For pressure, the fluctuations are wild, and
the autocorrelation
Hi Evelyne,
I haven't got a clue... But does it work if you use -settime when
concatenating the trajectories, to avoid having frames with the same time
index? It shouldn't cause a segfault, but it might.
Cheers,
Tsjerk
On Fri, Sep 6, 2013 at 7:20 AM, deplazes e.depla...@uq.edu.au wrote:
Hi
need to make a new index file that corresponds to the new ,
reduced .tpr file
Cheers
E
Enjoy Ausserberg
From: Tsjerk Wassenaar [via GROMACS]
ml-node+s5086n5011009...@n6.nabble.commailto:
ml-node+s5086n5011009...@n6.nabble.com
Date: Fri, 6 Sep 2013 02:12:25 -0700
To: Evelyne Deplazes
Hi Sri,
I guess that this simulation was run through the WeNMR GMX portal? It's not
really a Gromacs question. Problems with that portal should be directed to
the adminstrator, who will send it to me anyway, so I'll respond here :)
The error means 1. that I should put time in writing more clear
Hi Deepak,
You have to set the minimal distance between ions lower. Check the help of
genion.
Cheers,
Tsjerk
On Aug 28, 2013 8:04 AM, Deepak Ojha alwaysinthem...@gmail.com wrote:
Dear Gmxers,
I want to simulate 5M nabr aqueous solution.To add the ions I use genion
command and add 22 na and
Hey :)
Sorry for replying a bit late. But the issues you mention in this and the
other posts are usually solved by closely reading the text of the tutorial,
not only the commands.
Cheers,
Tsjerk
On Sun, Aug 25, 2013 at 3:44 AM, The One And Only chappybo...@gmail.comwrote:
Never mind, I'm
the topology file.
On Tue, Aug 27, 2013 at 1:33 PM, Tsjerk Wassenaar tsje...@gmail.com
wrote:
Hey :)
Sorry for replying a bit late. But the issues you mention in this and the
other posts are usually solved by closely reading the text of the
tutorial,
not only the commands.
Cheers
An editor is a program to edit the text in a file: gedit, nano, vi, emacs,
... It'll be the equivalent of Windows' Notepad. Can you find a tutor
around to help you out with the basic usage of Linux? It's always difficult
to plunge into several different things at the same time, here 'using
linux',
Hi Pooja,
Do you mean solvating around the protein, or placing water inside? If you
feel brave, you can check out the C code of genbox. Genbox copies a box of
solvent to cover the box with the protein, and then removes all solvent
which has overlaps with the protein.
Cheers,
Tsjerk
On Mon,
Hi Jonathan,
The itp's for the ligands were given atomtype sections, but atomtypes (and
other *types) may only be defined before any moleculetype definition (check
chapter 5 of the manual for the topology format). You'll need to remove
anything before the moleculetype directive from the itp files
Hi Kavya,
That shouldn be a problem. Please post your sequence of commands for
concatenating and further processing of the trajectory.
Cheers,
Tsjerk
On Thu, Aug 1, 2013 at 8:12 AM, Kavyashree M hmkv...@gmail.com wrote:
Dear users,
I ran a simulation for 25ns. First 5ns in 8 core machine
Hi Bipin,
If A/C have RMSD 0.4 nm, but A/B and B/C both have RMSD 0.3 nm, they'll
end up in the same cluster.
Cheers,
Tsjerk
On Wed, Jul 31, 2013 at 9:45 AM, bipin singh bipinel...@gmail.com wrote:
Thanks for the reply Prof. David. But in the output it shows that The RMSD
ranges from
Hi Jonathan,
I suspect the dash is not of the right kind. Did you by chance copy/paste
the command? Did you try typing it?
Cheers,
Tsjerk
On Sat, Jul 13, 2013 at 12:03 AM, Jonathan Saboury jsab...@gmail.comwrote:
I am following Tutorial 1 from
constraints
freeze_grps
virtual_sites
Cheers,
Tsjerk
On Jul 9, 2013 10:36 PM, Nash, Anthony anthony.n...@warwick.ac.uk wrote:
Hi all,
I would imagine this has been covered before, yet I don't think I have
unearthed the right search inquiry yet.
I want to make a dihedral angle along the
Hey :)
You can use editconf -scale to scale the system to the average box size.
Cheers,
Tsjerk
On Jul 9, 2013 4:28 PM, Mirco Wahab mirco.wa...@chemie.tu-freiberg.de
wrote:
On 09.07.2013 16:11, Neha wrote: I had a question about trjconv. After
one of my simulations has...
You could dump many
Hi Vinita,
I would guess that the other bond would not be made anyway according
to the criteria used by pdb2gmx. Or does it say it's making the bond?
Does the bond appear in the .top file?
Cheers,
Tsjerk
On 7/8/13, Vinita Kumari vinita2...@gmail.com wrote:
Dear gromacs users,
I want to break
Hi Shima,
You need to give a reference structure with the -s option. Otherwise the
program assumes you mean to use topol.tpr, which isn't present.
Cheers,
Tsjerk
On Sun, Jul 7, 2013 at 11:51 AM, Shima Arasteh
shima_arasteh2...@yahoo.comwrote:
Dear gmx users,
I' d like to get pdb files
Hi Cyrus,
In a rectangular box (which is a specific case of a triclinic box) your
molecule can't rotate freely without significant chance to run into its
periodic image, invalidating whatever result you get. So, unless rotation
is of no concern, or can be cirrcumvented, you'll need to use a
Hi Yutian Yang,
I don't think it's because of the size of the system. Can you run trjconv
without -pbc nojump? And did you check the trajectory with gmxcheck? Does
the output file exceed a maximum file size limit?
Hope it helps,
Tsjerk
On Wed, Jul 3, 2013 at 9:22 PM, Yutian Yang
Hi Richa,
From your explanation, I understand you want to know the sum of distances
between each frame and its corresponding filtered frame. I think it makes
more sense to sum squared distances, but that's a minor detail.
The (non-mass-weighted) RMSD between two structures, written as positional
Hi Melchor,
So what did you expect, what did you do, and what did you get?
Cheers,
Tsjerk
On Tue, Jul 2, 2013 at 2:45 PM, Melchor S. msm...@cid.csic.es wrote:
Hi all,
I am trying to calculate an RMSD of two simulations. All the setting are
equal for both, but i use OPLS in one and for
Hi Melchor,
Have you looked at the structures? The GROMOS people suggest using
twin-range cut-off with reaction field correction, and the Vanderwaals
cutoff you use seems a bit small, as 1.4 nm is commonly used with GROMOS.
Maybe that makes a difference.
Cheers,
Tsjerk
On Tue, Jul 2, 2013 at
Hi Silvia,
The .xtc file does not contain velocities. You'll need to use the .trr file.
Cheers,
Tsjerk
On Tue, Jul 2, 2013 at 8:25 PM, Silvia silviadilecc...@gmail.com wrote:
Dear users and experts,
I am new in the list and I am writing because I have a problem to get
velocities from the
Hi Sonika,
cmake needs a specification of the path where the source code is. In
addition to that, it is best to build it in a separate directory. As
explained on the website, in your gromacs directory:
mkdir build
cd build
cmake ../
make
make install
Hope it helps,
Tsjerk
On Tue, Jul 2,
where N is the number of atoms and n is the number of frames :p
T.
On Mon, Jul 1, 2013 at 8:29 AM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Ankita,
I should not answer questions before coffee!! Sorry.
It's the covariance matrix! So it's
1/n sum x1x1 1/n sum x1y1 1/n sum x1z1
1
ri dot delta rj so I don't think so I can use the
eigenvectors
Kind regards
Ankita
On Monday, July 1, 2013, Tsjerk Wassenaar wrote:
Hi Ankita,
The fie contains the eigenvectors as
x1 y1 z1
x2 y2 z2
...
xN yN zN
Hope it helps,
Tsjerk
On Mon, Jul 1, 2013 at 1:38
the first column wud have
alpha atom one second column would have 2nd aloha atom n third would have
correlation between them?
Kind regards,
Ankita
On Monday, July 1, 2013, Tsjerk Wassenaar wrote:
Hi Ankita,
I should not answer questions before coffee!! Sorry.
It's the covariance
Hi Shima,
You can use the same parameters. There is no difference other than the
position of atoms.
Cheers,
Tsjerk
On Mon, Jul 1, 2013 at 9:52 AM, Shima Arasteh
shima_arasteh2...@yahoo.comwrote:
Dear gmx users,
I have D amino acids in my input .pdb file. The force field which I aim to
Hi Ankita,
The fie contains the eigenvectors as
x1 y1 z1
x2 y2 z2
...
xN yN zN
Hope it helps,
Tsjerk
On Mon, Jul 1, 2013 at 1:38 AM, Ankita naithani ankitanaith...@gmail.comwrote:
Hi,
I wanted to know the exact format of covariance.dat file as generated by
g_covar during covariance
Hi Sainitin,
You can extract only the protein and ligand, using a suitable index file,
or you can limit the number of frames.
Cheers,
Tsjerk
On Thu, Jun 27, 2013 at 5:36 PM, Thales Kronenberger
kronenberg...@gmail.com wrote:
Don't you wanna try to use the VMD
use vmd xxx.gro yyy.trr and
Hi Yutian Yang,
Yes. That is, if the chain is interacting with itself. If it remains curled
up, then it won't be a problem.
Cheers,
Tsjerk
On Thu, Jun 27, 2013 at 10:10 PM, Yutian Yang yyan...@syr.edu wrote:
Hi all,
I have a question about PBC. If I have a polymer chain that is longer
Hi,
g_rmsf doesn't do distances. To answer the question, you can use g_rms with
-fit none and a suitable index group. Does depend a bit on what you mean
with distance. The distance traveled by a residue could well mean the
average distance for all particles in the residue, which is what you'll
Hey Thomas,
No, there is no such tool. Sorry.
May I ask how you did the MinVar fitting?
Cheers,
Tsjerk
On Mon, Jun 17, 2013 at 12:55 PM, Thomas Evangelidis teva...@gmail.comwrote:
Dear GROMACS list,
I used minVar to remove global rotations and translations from a
trajectory, but due to
Hi Maggin,
Why would that be a problem?
Tsjerk
On Mon, Jun 17, 2013 at 7:28 AM, maggin maggin.c...@gmail.com wrote:
Hi, all
I run a small peptide, and after NVT, I got the XXX.gro file like this,
http://gromacs.5086.x6.nabble.com/file/n5009205/next6_gro.bmp
because the peptide not at
Hi Maggin,
Okay, this image may require a bit of explanation :p VMD has drawn bonds
according to the bondedness in a reference file. But the atoms have moved,
and some went over the box boundaries. So they show up with long bonds
crossing the whole box. It's not a problem, just a visualization
Hi Maggin,
The constraints are typically used during MD simulation to allow larger
time steps.
Cheers,
Tsjerk
On Fri, Jun 14, 2013 at 9:39 AM, maggin maggin.c...@gmail.com wrote:
Hi, Tsjerk,
I have one question that in what situation people do constraint ?
Thank you very much!
maggin
Hi Maggin,
Why do you run EM with constraints?
Cheers,
Tsjerk
On Thu, Jun 13, 2013 at 10:53 AM, maggin maggin.c...@gmail.com wrote:
Hi, Justin,
It's seems no problem at steep energy minimization, except lose H atoms
connect with C, the superposition are very well.
When I use Pymol to
into protein
motions (Allosteric transitions, effector signalling??). It would however
be intensively complicated to derive for the whole protein considering mine
is a tetramer and a huge system.
Kind regards,
Ankita
On Sat, Jun 8, 2013 at 9:18 PM, Tsjerk Wassenaar tsje...@gmail.com
plots and also 3d
pdb projections. Could you please guide me in the right direction to
understand these 2d plots and infer the significant results?
Kind regards,
Ankita
On Thu, Jun 6, 2013 at 2:49 PM, Tsjerk Wassenaar tsje...@gmail.com
wrote:
Hi Ankita,
Please provide the commands
Hi Anirban,
The eigenvectors obtained from the simulation are a way of rewriting the
coordinates of your structures, not in terms of atoms-XYZ, but as
combinations of these. Because they are combinations of atom-positions,
they are defined for the selection of atoms used for the calculation. If
the crystal structure onto the
EV, then I need to consider only the CA atoms of the crystal structure
(which in that case won't be the exact crystal structure) as well. Right?
Thanks a lot again.
Regards,
Anirban
On Thu, Jun 6, 2013 at 3:56 PM, Tsjerk Wassenaar tsje...@gmail.com
wrote:
Hi
Hi Ankita,
Please provide the commands you've run and the screen output from g_covar.
Cheers,
Tsjerk
On Thu, Jun 6, 2013 at 3:44 PM, Ankita naithani ankitanaith...@gmail.comwrote:
Hi,
I wanted to know about the eigenvectors and eigenvalues. I recently
performed the principal component
to the
frame at time 0??
Because in the manual the rmsd equation show that reference structure
correspond to the time t=0 but the help doesn't confirm.
THanks a lot for your help,
2013/6/2 Tsjerk Wassenaar tsje...@gmail.com
Hi Nawel,
g_rmsdist calculates the RMSD of distances
Hey :)
Just center the bilayer around z=0, solvate and put all molecules in the
box with trjconv. Then add 10 to the PBC Z-component (third number from the
last line in the .gro file).
Cheers,
Tsjerk
On Mon, Jun 3, 2013 at 6:55 PM, Gunther Lukat g.lu...@gmx.net wrote:
You could try packmol
Hi Neha,
A single structure is like a trajectory with only one frame :p trjconv
works on those as well.
Right, set the center at 0,0,0 and choose the lipids as group for centering.
Cheers,
Tsjerk
On Mon, Jun 3, 2013 at 7:31 PM, Neha nshafi...@wesleyan.edu wrote:
Hi, thank you so much!
molecules in the box? Sorry
for
being so annoying need a lot of elaboration!
Tsjerk Wassenaar wrote
Hi Neha,
A single structure is like a trajectory with only one frame :p trjconv
works on those as well.
Right, set the center at 0,0,0 and choose the lipids as group for
centering
Hi Nawel,
g_rmsdist calculates the RMSD of distances, and distances are invariant to
translation and rotation.
Cheers,
Tsjerk
On Sun, Jun 2, 2013 at 1:45 PM, Nawel Mele nawel.m...@gmail.com wrote:
Hi,
THanks for your answers. I already seen the help for this command but when
its write
Hey,
If the gro file was built with a non-gmx program, it may be that the
numbers indeed broke the format, which then needs to be fixed. In case you
write your own program, you want to use a statement like atid = atid %1e5
to make sure it doesn't go over five digits. Correcting the format is
Hi Miguel,
Sorry for not responding earlier, but the question isn't really simple :)
What you do is determining the covariance matrix from the start up to a
certain point and see for different end points what the overlap is with the
covariance matrix from the whole. This means that in all cases,
to the end,
there will not be significant contributions to the covariance matrix.
Thanks for your valuable comments. Highly appreciated!
2013/5/30 Tsjerk Wassenaar tsje...@gmail.com
Hi Miguel,
Sorry for not responding earlier, but the question isn't really simple :)
What you do
No, the residue names are the those from the .top file. But that's not the
same as the moleculetypes. You have to change the residue names in the [
atoms ] section.
Cheers,
Tsjerk
On Sun, May 26, 2013 at 12:57 AM, Mark Abraham mark.j.abra...@gmail.comwrote:
AFAIK, the residue names in the
Hi Arunima,
In bash you can also combine the residue names and such with the RMSF graph:
paste (grep ^\(ATOM\|HETATM\) structure.pdb | cut -b 17-26 | uniq)
(grep ^[^#@] rmsf.xvg)
To make it a bit more clear, the redirection ( ... ) treats the output of
the command between parentheses as an
Hi Rajiv,
Square the values, sum them per residue and take the square root.
Cheers,
Tsjerk
On May 8, 2013 7:24 AM, 라지브간디 ra...@kaist.ac.kr wrote:
Dear gmx users,
I've done covariance matrix for backbone of protein using g_covar command.
Also, can able to plot all projections through
Hi Bipin Singh,
That indeed gives you the RMSD against the average. Do think about it a bit
more: do you want the average of the whole structure, or should you account
for a phase of relaxation?
Cheers,
Tsjerk
On Wed, Apr 24, 2013 at 2:17 PM, Justin Lemkul jalem...@vt.edu wrote:
On
Hi Anirban,
If you calculate the RMSD over a trajectory using g_rms and do block
averaging on the result, it won't give you any information about
convergence. The conformational space away from the reference structure
(0.1nm, 0.5nm?) is just too big. This means that the protein can be
moving a
Hey,
For the average distance matrix, you can use g_rmsdist.
Cheers,
Tsjerk
On Mon, Apr 15, 2013 at 6:19 PM, Justin Lemkul jalem...@vt.edu wrote:
On 4/15/13 12:08 PM, Steven Neumann wrote:
And last question:
Are these minimum distances averaged over the simulation time? Cannot find
http://gromacs.5086.x6.nabble.com/How-to-get-the-number-of-frames-contained-by-an-xtc-trajectory-file-td4998050.html
Cheers,
Tsjerk
On Tue, Apr 9, 2013 at 11:37 AM, Albert mailmd2...@gmail.com wrote:
Hello:
I am trying to extract last frame of my MD simulations with command:
trjconv_mpi
Hey :)
I'll make a try to be a bit more constructive :p
First of all, always try to think out of the box, especially with PBC :D
The problem may be due to overlapping atoms/molecules, pushing each other
out during energy minimization. When merging boxes, be careful not to
introduce overlaps, by
Hey Abhinav,
Your polymer seems to be one long molecule, which is made whole over PBC.
The result has nothing to do with EM.
Cheers,
Tsjerk
On Thu, Apr 4, 2013 at 11:37 AM, Abhinav Agrawal abhv.a...@gmail.comwrote:
I have a clay pdb file
http://s24.postimg.org/je3mvov9h/MMT.png
and a
There is no outside of the box.
Tsjerk
On Wed, Apr 3, 2013 at 4:51 PM, Abhinav Agrawal abhv.a...@gmail.com wrote:
Hi,
I have a polymer box on which I wish to apply energy minimization. However,
when I do energy minimization runs to polymer chain unravels and goes out
of the box. I guess
Hi,
The 3D structures are in the original trajectory.
If you want particular 3D structure, e.g. corresponding to a certain
projection, then look at the time corresponding to that particular
projection and extract the frame at that time.
Cheers,
Tsjerk
On Wed, Mar 6, 2013 at 5:13 PM, 라지브간디
Hi,
Then you have to do PCA on the whole structure.
Cheers,
Tsjerk
On Mar 7, 2013 3:15 AM, 라지브간디 ra...@kaist.ac.kr wrote:
Thank you for your reply.
Actually I have done PCA for backbone and wants to see the motion
projections of eigenvectors in 3d structure.
The original trajectory only
Hi Vandna,
Have you followed one of the tutorials? E.g.
http://md.chem.rug.nl/~mdcourse/molmod2012/ or one of Justin's?
It should give you al the background you need.
Cheers,
Tsjerk
On Sat, Feb 23, 2013 at 11:35 AM, vandna sharma vsha...@imtech.res.in wrote:
hi..thanx for the reply
as i am
PM, Tsjerk Wassenaar tsje...@gmail.comwrote:
Hi KT,
What do you mean with size?
- circumscribed radius: editconf
- radius of gyration: g_gyrate
- dimensions of fitting box: editconf
- volume: g_sas
Cheers,
Tsjerk
On Fri, Feb 8, 2013 at 5:55 AM, Kieu Thu Nguyen kieuthu2...@gmail.com
Hi Valentina,
Use pdb2gmx -ter
Cheers,
Tsjerk
On Wed, Feb 13, 2013 at 1:22 PM, Valentina Erastova
valentina.erast...@durham.ac.uk wrote:
Hello!
I am simulating Aspartate at pH 10, so it needs to be fully deprotonated
(COO-, COO- and NH2).
pdb2gmx allows to easily set side chains to be
average70-100ns.pdb -b 7 -e 10
Regards,
-Vivek.
On Sat, 9 Feb 2013, Tsjerk Wassenaar wrote:
Hi,
The commands would certainly help, including the commands for getting the
reference structure. Do note that the reference is the reference for
fitting, which is 'external', i.e
,
S = 1/N sum (x - ref) (x - ref)'
or
S = 1/(N-1) sum (x - ref) (x - ref)'
N: the number of frames
Which one is right?
2013/2/12 Tsjerk Wassenaar tsje...@gmail.com
Hi Vivek,
If you use the g_covar option -ref, you not only use the reference
structure for fitting, you use
Don't use the option -ref. I've explained the how and why extensively some
while ago.
Cheers,
Tsjerk
On Sun, Feb 10, 2013 at 11:26 AM, vivek modi modi.vivek2...@gmail.comwrote:
Message: 2
Date: Sat, 9 Feb 2013 23:36:20 +0530
From: bipin singh bipinel...@gmail.com
Subject: Re:
Hi Kenji,
You can remove the jumps/rewinds using 'trjconv -pbc nojump'.
Cheers,
Tsjerk
On Sat, Feb 9, 2013 at 4:45 AM, Kenji Mochizuki kmo...@ims.ac.jp wrote:
Dear All
I have performed MD run with periodic boundary condition,
which system is consist of water and LJ particles.
I would
to select the specific molecule for -pbc nojump ?
For example,
the coordinates of water molecules are rewind and the LJ particles are NOT
rewind ?
Regards
Kenji
- Original Message -
From: Tsjerk Wassenaar tsje...@gmail.com
To: Discussion list for GROMACS users gmx-users@gromacs.org
Hi,
The commands would certainly help, including the commands for getting the
reference structure. Do note that the reference is the reference for
fitting, which is 'external', i.e. provided by the user. This is not the
same as the structure used to calculate the deviations, which is the
average
Hi KT,
What do you mean with size?
- circumscribed radius: editconf
- radius of gyration: g_gyrate
- dimensions of fitting box: editconf
- volume: g_sas
Cheers,
Tsjerk
On Fri, Feb 8, 2013 at 5:55 AM, Kieu Thu Nguyen kieuthu2...@gmail.comwrote:
Dear all,
I want to calculate the size of the
trjconv -fit rot+trans
Cheers,
Tsjerk
On Thu, Feb 7, 2013 at 6:19 AM, Kavyashree M hmkv...@gmail.com wrote:
Dear users,
Which tool can be used to create a trajectory
of structures (from each frame) superimposed
on the first frame using the original traj.xtc file?
Thank you
kavya
--
settings or an unstable topology.
-Justin
On Thu, Jan 24, 2013 at 11:13 PM, Tsjerk Wassenaar tsje...@gmail.com
wrote:
Hi KT,
This is caused by another problem. Your system blew up. Check messages
before this one, and check the log for LINCS warnings.
Cheers,
Tsjerk
On Thu, Jan 24
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