Ioannis Beis wrote:
Dear gromacs users,
I am trying to center the trajectory of a bilayer in the rectangular
simulation box in the frame of my effort to calculate the bilayer
thickness with g_dist. According to the visualization, the upper layer
of the membrane lies on the lowest part of th
Dear gromacs users,
I am trying to center the trajectory of a bilayer in the rectangular
simulation box in the frame of my effort to calculate the bilayer
thickness with g_dist. According to the visualization, the upper layer
of the membrane lies on the lowest part of the box and the lower
does not change the result.So, do you have any suggestions ? Any help
in pointing out where I am doing wrong will be helpful.Jagannath
--- On Wed, 7/7/10, chris.neale at utoronto.ca utoronto.ca> wrote:
From: chris.neale at utoronto.ca
Subject: [gmx-users] problem with trjconv -pbc cluster
change the result.So, do you have any suggestions ? Any
help in pointing out where I am doing wrong will be helpful.Jagannath
--- On Wed, 7/7/10, chris.ne...@utoronto.ca wrote:
From: chris.ne...@utoronto.ca
Subject: [gmx-users] problem with trjconv -pbc cluster
To: gmx-users@gromacs.org
Date
PS:
you realize that trjconv -pbc cluster is never going to work unless
you actually have a cluster, right? So you can't start this procedure
near your initial dispersed state. You need to start at some time T
where you actually do have a cluster. Then you can try -dump T, -dump
(T+X), -d
Dear Jagannath:
There is, as far as I know, no way to fix this. Here's what you should do.
1. Let the space between your timesteps be X ps.
2. Use trjconv -pbc cluster -dump X -o out.gro
2b. if that doesn't work, try trjconv -pbc cluster -dump (X*2) -o out.gro
2c. if that doesn't work, try trjco
the program is in an
infinte loop.
Jagannath
--- On Wed, 7/7/10, Mark Abraham wrote:
From: Mark Abraham
Subject: Re: [gmx-users] problem with trjconv -pbc cluster
To: "Discussion list for GROMACS users"
Date: Wednesday, 7 July, 2010, 12:20 PM
- Original Message -
From:
- Original Message -
From: jagannath mondal
Date: Wednesday, July 7, 2010 16:36
Subject: [gmx-users] problem with trjconv -pbc cluster
To: gmx-users@gromacs.org
---
| > Hi, I had a system of surfectants which are started with
Hi, I had a system of surfectants which are started with an initial
configuration where all of them are well dispersed. Visual study of trajectory
shows they start aggregating and finally form two discrete micelles. To
quantify this micelle clusterization, I tried to use the suggestions present
nitu sharma wrote:
Dear all
I am on the final step of MD simulation of
membrane protein . the final mdrun has successfully completed after
that I have filtered the water from the system .next step is to convert
it in final pdb to view it in pymol for this I am using "t
Dear all
I am on the final step of MD simulation of membrane
protein . the final mdrun has successfully completed after that I have
filtered the water from the system .next step is to convert it in final pdb
to view it in pymol for this I am using "trjconv" in this step I h
> Hi all,
> I am trying to use *trjconv command for -pbc but POPC molecules are
> breaking
> when visualize in VMD. The commands used are
> grompp -f pr.mdp -c em_out.gro -p .top -n index.ndx -o out.tpr
> trjconv -f em_out.gro -s out.tpr -o trj_out.gro -pbc inbox or cluster
> or
> whole
> T
Quoting sudheer babu <[EMAIL PROTECTED]>:
> Hi all,
> I am trying to use *trjconv command for -pbc but POPC molecules are breaking
> when visualize in VMD. The commands used are
> grompp -f pr.mdp -c em_out.gro -p .top -n index.ndx -o out.tpr
> trjconv -f em_out.gro -s out.tpr -o trj_out.gr
Hi all,
I am trying to use *trjconv command for -pbc but POPC molecules are breaking
when visualize in VMD. The commands used are
grompp -f pr.mdp -c em_out.gro -p .top -n index.ndx -o out.tpr
trjconv -f em_out.gro -s out.tpr -o trj_out.gro -pbc inbox or cluster or
whole
Thi trj_out.gro con
Hi Aline,
You probably missed the part of David's answer that this was probably
fixed in CVS code already? In that case:
This has probably been fixed in CVS code already. Some silly bug, no
particular reasons not to give you a frame at 100ps.
Tsjerk
On 4/25/07, Aline Rossi <[EMAIL PROTECTED]> w
*
**I have a 100ps .trr file. If I use:
**trjconv -f in.trr -o out.gro -dump 95 -s in.tpr
**
**trjconv stops returning the following warning:
**"Reading frame 20 time 95.000
**
**WARNING no output, trajectory ended at 100"
**
**
**Same warning if I -dump with any other value, as well with -
Aline wrote:
* Greetings,
*>*
*>* I have a 100ps .trr file. If I use:
*>* trjconv -f in.trr -o out.gro -dump 95 -s in.tpr
*>*
*>* trjconv stops returning the following warning:
*>* "Reading frame 20 time 95.000
*>*
*>* WARNING no output, trajectory ended at 100"
*>*
*>*
*>* Same warning i
Aline wrote:
Greetings,
I have a 100ps .trr file. If I use:
trjconv -f in.trr -o out.gro -dump 95 -s in.tpr
trjconv stops returning the following warning:
"Reading frame 20 time 95.000
WARNING no output, trajectory ended at 100"
Same warning if I -dump with any other value, as well
Greetings,
I have a 100ps .trr file. If I use:
trjconv -f in.trr -o out.gro -dump 95 -s in.tpr
trjconv stops returning the following warning:
"Reading frame 20 time 95.000
WARNING no output, trajectory ended at 100"
Same warning if I -dump with any other value, as well with -b 95 -e 95
OZGE ENGIN wrote:
Hi,
First of all, thank you for your attention. I used g_hbond in order to analyze
hydrogen bonds formed;but, I need a more detailed information. The command that
you mentioned is capable of giving information about hydrogen bonds formed in
each frame. However, I want to in
To: "Discussion list for GROMACS users"
Date: Wed, 28 Feb 2007 17:52:34 +0100
Subject: Re: [gmx-users] problem with trjconv
Hi Ozge,
Why do you first want to go to a .pdb trajectory? Gromacs comes with
g_hbond, which can analyze hydrogen bonds for you, as well as giving
you an index
Hi Ozge,
Why do you first want to go to a .pdb trajectory? Gromacs comes with
g_hbond, which can analyze hydrogen bonds for you, as well as giving
you an index file containing the atoms involved in hydrogen bonds,
which you can use to extract those from your trajectory. In addition,
g_hbond also
OZGE ENGIN wrote:
Hi,
I have a problem with the trjconv command.
I performed a 30 ns simulation, and wanted to analyze hydrogen bonds formed
between protein and water molecules. In this respect, I converted the xtc file
into a pdb file by selecting system option. As you can understand the o
Hi,
I have a problem with the trjconv command.
I performed a 30 ns simulation, and wanted to analyze hydrogen bonds formed
between protein and water molecules. In this respect, I converted the xtc file
into a pdb file by selecting system option. As you can understand the overall
file was such
erk Wassenaar" <[EMAIL PROTECTED]>
> Subject: Re: [gmx-users] Problem with trjconv centering after fitting
> To: "Discussion list for GROMACS users"
> Message-ID:
> <[EMAIL PROTECTED]>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
Hi,
Would that be the same? What happened here is that the system was
first fitted. Thus, the system is rotated and any operation concerning
pbc after that point will be screwed up, because the box definition
does not match the system. Solution: first perform all operations
involving pbc, then fi
[EMAIL PROTECTED] wrote:
Starting from a rhombic dodecahedron xtc file,
trjconv -fit rot+trans -f a.xtc -s a.tpr -o a_fit.xtc
trjconv -center rect -pbc whole -f a_fit.xtc -s a.tpr -o a_fit_cent.xtc
Visualization of a.xtc and a_fit.xtc via VMD are as expected. Nevertheless,
a_fit_cent.xtc shows
Starting from a rhombic dodecahedron xtc file,
trjconv -fit rot+trans -f a.xtc -s a.tpr -o a_fit.xtc
trjconv -center rect -pbc whole -f a_fit.xtc -s a.tpr -o a_fit_cent.xtc
Visualization of a.xtc and a_fit.xtc via VMD are as expected. Nevertheless,
a_fit_cent.xtc shows overlapping atoms and regio
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