Hi all,
I am planning to run a 100ns simulation by continuing a simulation in
increments of 1ns. After each round, analyses are performed and the
trajectory scrapped. One of the analysis I need to do is mean square
displacement; for this I need a continuous trajectory as provided by
trjconv
Hi Pablo,
You can use trjcat to stitch the parts of your trajectory together.
A .cpt file contains information about the state, the positions and such.
It doesn't contain static information, like residue/atom names, which are
needed for a reference structure.
Cheers,
Tsjerk
On Thu, Nov 22,
Hi,
I have run simulation of a large solute in a box of water. Trying to look at
the simulation output I used trjconv with and without the -pbc nojump option.
For example:
(1) trjconv_d -s md_100ns.tpr -f md_100ns.xtc -o md_100ns_noPBC_pbcmol.pdb
-pbc mol -ur compact
(2) trjconv_d -s
On 11/12/2011 11:23 PM, Efrat Exlrod wrote:
Hi,
I have run simulation of a large solute in a box of water. Trying to
look at the simulation output I used trjconv with and without the
-pbc nojump option.
For example:
(1) trjconv_d -s md_100ns.tpr -f md_100ns.xtc
-o
Hi,
You should use trjconv in 2 steps:
(1) trjconv_d -s md_100ns.tpr -f md_100ns.xtc -o
md_100ns_pbc_nojump.xtc -pbc nojump
in this step, select system for output
(2) trjconv_d -s md_100ns.tpr -f md_100ns_pbc_nojump.xtc -o
md_100ns_pbc_mol_center.xtc -pbc mol -center
in this step, select
Dear Gmx Users,
I am trying to convert my trajectory using trjconv. My system is made of 10
ligands and protein. Protein is jumping
divided into parts. The same is with my ligands. I am confused about the
point 2 and 3:
2. Extract the first frame from the trajectory as reference for removing
Steven Neumann wrote:
Dear Gmx Users,
I am trying to convert my trajectory using trjconv. My system is made
of 10 ligands and protein. Protein is jumping
divided into parts. The same is with my ligands. I am confused about the
point 2 and 3:
2. Extract the first frame from the
Hi,
You don't need a .tpr file for removing jumps; a pdb/gro file will do.
Cheers,
Tsjerk
On Oct 24, 2011 2:51 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Steven Neumann wrote: Dear Gmx Users, I am trying to convert my
trajectory using trjconv. ...
trjconv -dump 0
3. Remove jumps if
Sorry guys but I do not get this...
I used:
1. First make your molecules whole if you want them whole
trjconv -f md2.trr -s md2.tpr -pbc whole -o md2whole.xtc (I have chosen my
whole system for input and output)
2. I do not need cluster anything
3. Extract the first frame from the
Hi Steven,
Output can also be .pdb or .gro
Cheers,
Tsjerk
On Oct 24, 2011 3:59 PM, Steven Neumann s.neuman...@gmail.com wrote:
Sorry guys but I do not get this...
I used:
1. First make your molecules whole if you want them whole
trjconv -f md2.trr -s md2.tpr -pbc whole -o md2whole.xtc
Thank you both!!!
Steven
On Mon, Oct 24, 2011 at 3:01 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Steven,
Output can also be .pdb or .gro
Cheers,
Tsjerk
On Oct 24, 2011 3:59 PM, Steven Neumann s.neuman...@gmail.com wrote:
Sorry guys but I do not get this...
I used:
1.
Last question:
I would like to visualise my whole trjajectory looking at one of the ligands
only which stacked to the loop of my protein. Which option of trjconv will
be suitable to see whole trajectory of this ligand withoout any shifts on
the screen so I will be able to produce a movie? I
Steven Neumann wrote:
Last question:
I would like to visualise my whole trjajectory looking at one of the
ligands only which stacked to the loop of my protein. Which option of
trjconv will be suitable to see whole trajectory of this ligand withoout
any shifts on the screen so I will be
On 09/11/10 21:36, Justin A. Lemkul wrote:
I am doing REMD simulations of multiple homopolymeric peptides in a
PBC box, in vacuum (it's a custom coarse grain). GROMACS 4.0.5. I want
to analyze features of the system that require to use g_gyrate to find
out the moments of inertia of the system,
On 09/11/10 21:36, Justin A. Lemkul wrote:
There are numerous -pbc options with trjconv; have you tried others? I
have never had luck with -pbc nojump actually working, and -pbc atom
provides no guarantee that molecules will be properly reconstructed.
Using -pbc mol -center is often a much
ms wrote:
On 09/11/10 21:36, Justin A. Lemkul wrote:
There are numerous -pbc options with trjconv; have you tried others? I
have never had luck with -pbc nojump actually working, and -pbc atom
provides no guarantee that molecules will be properly reconstructed.
Using -pbc mol -center is
On 10/11/10 21:34, Justin A. Lemkul wrote:
ms wrote:
On 09/11/10 21:36, Justin A. Lemkul wrote:
There are numerous -pbc options with trjconv; have you tried others? I
have never had luck with -pbc nojump actually working, and -pbc atom
provides no guarantee that molecules will be properly
ms wrote:
On 10/11/10 21:34, Justin A. Lemkul wrote:
ms wrote:
On 09/11/10 21:36, Justin A. Lemkul wrote:
There are numerous -pbc options with trjconv; have you tried others? I
have never had luck with -pbc nojump actually working, and -pbc atom
provides no guarantee that molecules will
On 10/11/10 22:28, Justin A. Lemkul wrote:
First, let me see if I understand it correctly. From your explanation
(and intuition), it seems that the issue is that center of mass in a
periodic environment is ambiguous -there are always (at least) two
alternate configurations that have the center
Hi,
I am doing REMD simulations of multiple homopolymeric peptides in a PBC
box, in vacuum (it's a custom coarse grain). GROMACS 4.0.5. I want to
analyze features of the system that require to use g_gyrate to find out
the moments of inertia of the system, for example.
I understand g_gyrate
ms wrote:
Hi,
I am doing REMD simulations of multiple homopolymeric peptides in a PBC
box, in vacuum (it's a custom coarse grain). GROMACS 4.0.5. I want to
analyze features of the system that require to use g_gyrate to find out
the moments of inertia of the system, for example.
I
Hi gromacs users
I want to know after using trjconv -pbc, box disappears and solvent molecule
recedes from solute. is it true?
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
Dear Justin
thanks for your attentions
In my case, after md simulation my protein diffuse out from one side of box.
for solution I used trjconv -pbc nojump. then problem fixed but box
disappears and water molecules recedes from protein.
--
gmx-users mailing listgmx-users@gromacs.org
shahab shariati wrote:
Dear Justin
thanks for your attentions
In my case, after md simulation my protein diffuse out from one side of
box. for solution I used trjconv -pbc nojump. then problem fixed but box
disappears and water molecules recedes from protein.
That sounds like the
shahab shariati wrote:
Dear Justin
in my case only -pbc nojump fix problem. my purpose is not
visualization. do this xtc file ,in which protein diffuse out from box,
cause any problem in analysis? if yes, how can I fix it?
This same question has come up several times within the last
Hi gmx users
Perhaps, this question be repetitive. I want to know using trjconv -pbc is
only a solution for visualization problem? Is there
feasibility to use old trajectory file (with out trjconv -pbc) for any kind
of analysis without any problem?
--
Atila Petrosian
Ph.D. student of BioPhysical
atila petrosian wrote:
Hi gmx users
Perhaps, this question be repetitive. I want to know using trjconv -pbc
is only a solution for visualization problem? Is there
feasibility to use old trajectory file (with out trjconv -pbc) for any
kind of analysis without any problem?
Most Gromacs
Hi everyone,
please I'm doing a simulation of a dimer with a ligand.
When I want to visualize my trajectory, I have the problem that my dimer or
my ligand or both diffuse out of the box and I don't have a continuous
trajectory.
I tried many options:
1)trjconv -center -pbc mol -ur compact
Carla Jamous wrote:
Hi everyone,
please I'm doing a simulation of a dimer with a ligand.
When I want to visualize my trajectory, I have the problem that my dimer
or my ligand or both diffuse out of the box and I don't have a
continuous trajectory.
I tried many options:
1)trjconv -center
I thought I was sure -pbc cluster will work, but it doesn't :( trjconv get's
stuck on an infinite loop while calculating center of mass.
In an index.ndx I created a new group which I called CLUSTER, as Mark suggested
(I used make_ndx), then I ran trjconv:
trjconv -f 1Y2Elig_em.trr -s
Search:
trjconv pbc cluster
on the gromacs mailing list and take a look at the first hit.
Basically, you need to find a frame that *does* work with -pbc cluster
and then make a new .tpr based on the clustered .gro and then run
trjconv -pbc mol. Just ensure that this frame is as close to the
Thank you, Mark, for your tip, the indexing solution is perfect!
Regards,
Vis
--- On Tue, 12/22/09, Mark Abraham mark.abra...@anu.edu.au wrote:
From: Mark Abraham mark.abra...@anu.edu.au
Subject: Re: [gmx-users] trjconv -pbc: how to keep all parts of the system
clustered together in PDB
Dear GROMACS users and gurus,
I am sorry if it's a stupid question...I'm fairly new GROMACS, and something is
been driving me crazy. I have a protein, two metal ions, and inhibitor in my
system. Somehow in some of the frames I can't keep all those pieces clustered
compactly for some
Visvaldas K. wrote:
Dear GROMACS users and gurus,
I am sorry if it's a stupid question...I'm fairly new GROMACS, and something is been
driving me crazy. I have a protein, two metal ions, and inhibitor in my system. Somehow
in some of the frames I can't keep all those pieces clustered
Hi,
I've tried using trjconv -pbc nojump with a .tpr created from the first
frame of the trajectory (clustered so the vesicle should be whole). The
output trajectory starts with a complete vesicle, but small numbers of
lipid particles progressively move to places outside of the box. By the
Hi Daniel,
The problem is likely that your vesicle is interacting with itself
over the periodic boundaries. There are regions where there is no
solvent inbetween. That means that lipids can go over from one image
to the other by diffusion, which will not be compensated by using -pbc
nojump. You
Ok, I guess in future I will have to make sure the box is big enough to contain
the entire vesicle in the triclinic representation. It's kind of a shame
though, as the main reason for using the rhombic dodecahedron box was to
minimize the amount of bulk solvent required.
Thanks for your help
Hi Daniel,
1a. I am confused about what is your vesicle. Is it everything that
you are showing in these images? Or perhaps it is only the cyan thing
that I can see sliced through in:
http://img109.imageshack.us/img109/8227/trajenddat.jpg
1b. I suspect that the cyan ring encircled by
There is no problem with the rhombic dodecahedron in and of itself.
Note that editconf -d does not actually yield the -d that you ask it
to and that it errs on different sides of your request for different
box types. To prove this to yourself, run your starting structure
through editconf
Hi,
I am running a coarse-grained simulation of a lipid vesicle (~70,000
particles), using a rhombic dodecahedron box to limit the amount of
solvent I require. The vesicle (unsurprisingly) moves over the periodic
boundaries during the simulation. Various analyses I am conducting
require
Hi,
Thanks for the suggestion to use trjconv -pbc nojump. Unfortunately, it
has not worked, as the vesicle is still not whole in the trajectory. I
have tried subsequently centering the trajectory, and representing the
system with -ur compact, but still it does not work. I am wondering if
the
Hi Daniel,
If the structure is correct in the coordinate file you used as input
to generate the .tpr, you can use that structure as reference to
trjconv, using -pbc nojump.
Cheers,
Tsjerk
On Mon, Nov 30, 2009 at 6:17 PM, Daniel Parton
daniel.par...@bioch.ox.ac.uk wrote:
Hi,
Thanks for the
Hi Daniel,
I think you still need to read and attempt what has already been
suggested. To be more explicit:
trjconv -f a.xtc -o a_cluster.gro -e 0.001 -pbc cluster
grompp -f a.mdp -c a_cluster.gro -o a_cluster.tpr
trjconv -f a.xtc -o a_cluster.xtc -s a_cluster.tpr -pbc nojump
from:
Hi,
trjconv -f a.xtc -o a_cluster.gro -e 0.001 -pbc cluster
You might want to use -dump to extract a specific frame, rather than using -e:
trjconv -f a.xtc -o a_cluster.gro -pbc cluster -dump 0
Also, do mind that for a subsequent call to trjconv, using -pbc nojump
and the extracted frame as
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
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.
I am very sure that the ligand has attached to the protein.
with this command =
trjconv -pbc nojump -center rect
so,
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.
I am very sure that the ligand has attached to the protein.
with this command =
trjconv -pbc
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. I supposed that the ligands
dock/attach on the protein.
I want to center the protein and see if the ligands dock/attach on the
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. I supposed that the ligands
dock/attach on the protein.
I want to center the protein and see if the ligands
Hi,
I answered a very similar question last week but it appears that
gmx-users is not online by now: try to use this script. And be aware
to re-wrap code lines as my mail splits it. Please comment if it
actually works for you.
Best.
Daniel
***
Usage notes:
- Just copy/and/paste the
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 atom -center rect
the most part of the protein is still in the right edge of the box
the small
Hi:
I equilibrated a DPPC membrane that I built. I want to take a
snapshot for doing some protein-membrane simulations, but first i have
to do somethings for eliminating the lipids out of the box. I have
tried with pbc and fit options like people say in the list and it
doesn't work. Anybody can
If you use the new version of Gromacs (3.3.3), there are several options that
work nicely. Try each of them separately, probably one of them will work, maybe
a combination will be necessary based on how much your lipids jump around.
trjconv -center
(choose DPPC for centering)
trjconv -pbc
Thanks for the quickly answer. I used 3.3.3 and 3.3.1 version and the
lipids of a monocape are above to the other. The lipids are jumping yet
after all those changes. I proved each option separately and some
combinations of them.
trjconv -s a.tpr -f a.xtc -o b.xtc -center
trjconv -s a.tpr -f
Hello all,
I have tried using trjconv -pbc(all options) to get a continuous
trjactoary visulations on VMD. I am modeling an 11 residue receptor
antiparellel to itself and one of the receptor strand jumps outside the
box sometimes.
I have used search to solve the problem but everthing i tried
Hi Belquis,
You have to give trjconv a reference structure in which the parts are
together and which is close to the starting configuration. This has
been mentioned on the list before. For more information, search the
archives on trjconv and/or periodic boundary conditions (and possibly
my
Hi Tsjerk,
Thank you for replying. I did give it a reference structure where the two
parts are together. I solved the problem finally!
I had a 10ns simulation before that and I used -pbc nojump on the original
trjactory and it worked fine..but when I did it for the extra 10 ns i ran,
it didnt
Hello all,
I have tried using trjconv -pbc(all options) to get a continuous
trjactoary visulations on VMD. I am modeling an 11 residue receptor
antiparellel to itself and one of the receptor strand jumps outside the
box sometimes.
I have used search to solve the problem but everthing i
Hi Belquis,
Just some background on the issue. The reason that your solution
worked, and therefore the failure of your first procedure, is that in
the second case the frame at t=10ns was modified using the frame at
t=10-timestep ns as reference, whereas the modification in the first
case was
Hi Mauricio,
That this seems to work best for you is, sorry to say, just between
the ears. I'm not completely sure, but I think the implementation was
done correctly, so as to first deal with pbc related options, before
fitting. In that case, the results would be the same as running
trjconv
Hi TSjerk,
Thanks for the explaination. It is appreciated.
Belquis
Hi Belquis,
Just some background on the issue. The reason that your solution
worked, and therefore the failure of your first procedure, is that in
the second case the frame at t=10ns was modified using the frame at
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