Liu Shiyong wrote:
Dear all,
I tried to output protein-ligand complex from trr file .
Could I select both Group 2 and Group 12 at the same time ?
Or I have to run this command for every group , respectively?
Use make_ndx to merge the groups and pass the index file to trjconv.
-Justin
Hi,
I am having a problem with trjconv to get a single snap-shot from a
trajectory
file. I am using gromacs 4.0.7 .
If I try to get a snapshot corresponding to 14 ps, I was trying to use -b 14
-e 14 command as follows. But,
If I issue this command as shown below
trjconv --f traj.xtc -o
Sanku M wrote:
Hi,
I am having a problem with trjconv to get a single snap-shot from a
trajectory file. I am using gromacs 4.0.7 .
If I try to get a snapshot corresponding to 14 ps, I was trying to use
-b 14 -e 14 command as follows. But,
If I issue this command as shown below
trjconv
, trajectory ended at 14'
Any help will be appreciated.
Sanku
From: Justin A. Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Thu, May 5, 2011 10:22:38 AM
Subject: Re: [gmx-users] trjconv problem
Sanku M wrote:
Hi,
I am
I found it will work if I use -b 13.9 -e 14.1
From: Sanku M msank...@yahoo.com
To: jalem...@vt.edu; Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Thu, May 5, 2011 10:33:19 AM
Subject: Re: [gmx-users] trjconv problem
Hi Justin,
In many
*To:* jalem...@vt.edu; Discussion list for GROMACS users
gmx-users@gromacs.org
*Sent:* Thu, May 5, 2011 10:33:19 AM
*Subject:* Re: [gmx-users] trjconv problem
Hi Justin,
In many of the frames, if I use -b and -e to be same , it works
For example, I found if I use -b 16 -e 16, it gives me
Hi Алексей,
We have no use for your PDB files anyway :) In order not to loose the
phospho from your tyrosine, you want to start out with trjconv -pbc
whole. To obtain what you desire, you probably want to give the
following a good read:
I am trying to use trjconv to extract frames from my protein/membrane system
in order to analyse with gdmat. Before using git's latest gromacs version,
everything worked just fine. But now, every coordinate file trjconv gives me
has the DPPC lipid molecules without numbering. It is like if my
numbering single-residue molecules.
If you also want you lipids to continue numbering, you'll have to set the
env.var. GMX_MAXRESRENUM
to the number of residues in a lipid.
Berk
Date: Mon, 18 Jan 2010 13:05:42 -0200
From: stefh...@gmail.com
To: gmx-users@gromacs.org
Subject: [gmx-users] trjconv problem
in a lipid.
Berk
Date: Mon, 18 Jan 2010 13:05:42 -0200
From: stefh...@gmail.com
To: gmx-users@gromacs.org
Subject: [gmx-users] trjconv problem
I am trying to use trjconv to extract frames from my protein/membrane
system
don't get though.
In the problematic output the lipids can not be one single residue, but should
be two or more residues.
Berk
Date: Mon, 18 Jan 2010 10:31:19 -0500
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] trjconv problem
Could renumbering be a switchable
Hi,
thanks for the tips. First I used the information of the exact time I got from
g_cluster which did not work (t=5590.093). So I used trjconv to convert the
whole trajectory in a pdb-file from which I got the exact time (t=5590.00049)
of the frame to be extracted that was different compared
Hi everybody,
I am trying to extract some frames from my md simulation using trjconv. For
some frames this works fine but for others of the same simulation I get the
following error message (for frame after 5590 picoseconds):
Skipping frame500 time 5250.000
Setting output precision to
hi,
similar happened to me, when i used the -b and -e flags of trjconv. to me it
seemed that if you do not hit exactly the time frame as written in the trr
file, trjconv will not output anything. when i used the -dump flag it worked,
because then frames near the specified time are dumped.
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