From: [EMAIL PROTECTED] <[EMAIL PROTECTED]>
Subject: gmx-users Digest, Vol 55, Issue 150
To: [email protected]
Date: Friday, November 28, 2008, 11:21 PM
Send gmx-users mailing list submissions to
[email protected]
To subscribe or unsubscribe via the World Wide Web, visit
http://www.gromacs.org/mailman/listinfo/gmx-users
or, via email, send a message with subject or body
'help' to
[EMAIL PROTECTED]
You can reach the person managing the list at
[EMAIL PROTECTED]
When replying, please edit your Subject line so it is more
specific
than "Re: Contents of gmx-users digest..."
Today's Topics:
1. Re: Analyzing a trajectory split over multiple files
(TJ Piggot)
2. Re: Fatal error with grompp(with detail process)
(Justin A. Lemkul)
3. Re: Re: Re: defination of cluster (Justin A. Lemkul)
4. RE: Box vector shifts number in x and y/z dimension
(Berk Hess)
----------------------------------------------------------------------
Message: 1
Date: Fri, 28 Nov 2008 11:47:55 +0000
From: TJ Piggot <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] Analyzing a trajectory split over
multiple
files
To: Discussion list for GROMACS users
<[email protected]>
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain; charset=iso-8859-1; format=flowed
Just as a note most analysis tools have a -noxvgr option to
output the
results without any of the formatting information for
grace.
Also I still think the easiest way to solve your problem is
to just
initially use trjcat to concatenate your trajectory, then
run the analysis
on this.
Tom
--On Friday, November 28, 2008 05:06:31 +0530 Suman
Chakrabarty
<[EMAIL PROTECTED]> wrote:
On Fri, Nov 28, 2008 at 4:24 AM, Nicolas
<[EMAIL PROTECTED]> wrote:
Suman Chakrabarty a écrit :
It would have been much easier if there was
some way to concatenate
the multiple .xvg files easily. Also, the
analysis programs should be
able to export the output data in raw 2 (or
more) column format
without all the formatting statements as an
option.
Actually, there is:
grep -v "^#" *.xvg > concatenate.xvg
The -v "^#" will skip all the comment
lines of your xvg files. Of course,
this assumes that your xvg files are correctly
named, i.e. file01.xvg,
file02.xvg, etc. With a short shell script, you
can easily re-add the
comments at the beginning of your concatenate
file, renumber the frames
correctly, etc. It is more convenient to write a
Python or a Perl script
to do this kind of stuff, though.
Nicolas
Thank you very much! I always knew there must be
something smart to be
done. I should now delve into the nitty-gritty of
scripting. grep
seems to be a particularly useful tool! :)
Regards,
Suman.
----------------------
TJ Piggot
[EMAIL PROTECTED]
University of Bristol, UK.
------------------------------
Message: 2
Date: Fri, 28 Nov 2008 07:25:28 -0500
From: "Justin A. Lemkul" <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] Fatal error with grompp(with
detail process)
To: Discussion list for GROMACS users
<[email protected]>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Jenny Hsu wrote:
Hi all:
I have a problem with grompp
I want to making "POPC+protein" file
and I search the archieve and follow the process
1.run pdb2gmx for protein only
2.add below parameters into my topology file
#include "ffG53a6.itp"
#include "lipid.itp"
#include "popc.itp"
3.adjust the [ molecules ] section to list the number
and type of my
components
4.run editconf and genbox
5.run grompp and it shows
Fatal error:
Atomtype CA not found
We just had a discussion about this:
http://www.gromacs.org/pipermail/gmx-users/2008-November/038282.html
You can copy the relevant portions of lipid.itp into the
appropriate sections in
ffG53a6nb.itp/ffG53a6bon.itp. Otherwise, including the
files as you have will
not work.
-Justin
*Below is all information it shows*
*Can someone help me to solve this problem?*
*I am appreciate with that.*
*Thaks.*
:-) G R O M A C S (-:
Getting the Right Output Means no Artefacts in
Calculating Stuff
:-) VERSION 4.0 (-:
Written by David van der Spoel, Erik Lindahl,
Berk Hess, and others.
Copyright (c) 1991-2000, University of
Groningen, The Netherlands.
Copyright (c) 2001-2008, The GROMACS
development team,
check out http://www.gromacs.org
<http://www.gromacs.org/>
for more information.
This program is free software; you can
redistribute it and/or
modify it under the terms of the GNU General
Public License
as published by the Free Software Foundation;
either version 2
of the License, or (at your option) any
later version.
:-) grompp (-:
Option Filename Type Description
------------------------------------------------------------
-f em.mdp Input, Opt! grompp input file
with MD parameters
-po mdout.mdp Output grompp input file
with MD parameters
-c 1UEO-nowater_water.gro Input Structure
file: gro g96 pdb
tpr tpb
tpa
-r conf.gro Input, Opt. Structure file: gro
g96 pdb tpr tpb tpa
-rb conf.gro Input, Opt. Structure file: gro
g96 pdb tpr tpb tpa
-n index.ndx Input, Opt. Index file
-p 1UEO-nowater.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o 1UEO-nowater_em.tpr Output Run input file:
tpr tpb tpa
-t traj.trr Input, Opt. Full precision
trajectory: trr trj cpt
-e ener.edr Input, Opt. Energy file: edr ene
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-nice int 0 Set the nicelevel
-[no]v bool yes Be loud and noisy
-time real -1 Take frame at or first
after this time.
-[no]rmvsbds bool yes Remove constant bonded
interactions with virtual
sites
-maxwarn int 0 Number of allowed warnings
during input
processing
-[no]zero bool no Set parameters for bonded
interactions without
defaults to zero instead
of generating an error
-[no]renum bool yes Renumber atomtypes and
minimize number of
atomtypes
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Back Off! I just backed up mdout.mdp to
./#mdout.mdp.2#
checking input for internal consistency...
processing topology...
Opening library file
/usr/local/md/share/gromacs/top/ffG53a6.itp
Opening library file
/usr/local/md/share/gromacs/top/ffG53a6nb.itp
Opening library file
/usr/local/md/share/gromacs/top/ffG53a6bon.itp
Opening library file
/usr/local/md/share/gromacs/top/ff_dum.itp
WARNING 1 [file lipid.itp, line 14]:
Overriding atomtype LO
WARNING 2 [file lipid.itp, line 15]:
Overriding atomtype LOM
WARNING 3 [file lipid.itp, line 16]:
Overriding atomtype LNL
WARNING 4 [file lipid.itp, line 17]:
Overriding atomtype LC
WARNING 5 [file lipid.itp, line 18]:
Overriding atomtype LH1
WARNING 6 [file lipid.itp, line 19]:
Overriding atomtype LH2
WARNING 7 [file lipid.itp, line 20]:
Overriding atomtype LP
WARNING 8 [file lipid.itp, line 21]:
Overriding atomtype LOS
WARNING 9 [file lipid.itp, line 22]:
Overriding atomtype LP2
WARNING 10 [file lipid.itp, line 23]:
Overriding atomtype LP3
WARNING 11 [file lipid.itp, line 24]:
Overriding atomtype LC3
WARNING 12 [file lipid.itp, line 25]:
Overriding atomtype LC2
WARNING 13 [file lipid.itp, line 108]:
Overriding non-bonded parameters,
old: 0.00238804 3.38411e-06 new
LNL C 1 2.387718e-03 2.389594e-06
-------------------------------------------------------
Program grompp, VERSION 4.0
Source code file: toppush.c, line: 793
Fatal error:
Atomtype CA not found
--
Jenny Hsu, Biotechnology Dept.,
Ming Chuan University, Taiwan, R.O.C
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the
list. Use the
www interface or send it to
[EMAIL PROTECTED]
Can't post? Read
http://www.gromacs.org/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
------------------------------
Message: 3
Date: Fri, 28 Nov 2008 07:29:12 -0500
From: "Justin A. Lemkul" <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] Re: Re: defination of cluster
To: [EMAIL PROTECTED], Discussion list for GROMACS
users
<[email protected]>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=UTF-8; format=flowed
Q. Y. HUAN wrote:
Dear Mark and all,
Yes, I read it before I start. It states that the
program computes the size distributions of molecular/atomic
clusters in gas phase. Is it means that even a single
molecule, it is also defined as a cluster?
Thanks for the help.
In my mind, that would make no sense. Also, think about
your results that you
told us about - 8 micelles, and 8 aggregates detected. Do
you think that the
monomers are being considered?
-Justin
QIU YI HUAN
DEPARTMENT OF CHEMISTRY,
FACULTY OF SCIENCE,
UNIVERSITY PUTRA MALAYSIA,
MALAYSIA.
--- On Fri, 11/28/08, [EMAIL PROTECTED]
<[EMAIL PROTECTED]> wrote:
From: [EMAIL PROTECTED]
<[EMAIL PROTECTED]>
Subject: gmx-users Digest, Vol 55, Issue 147
To: [email protected]
Date: Friday, November 28, 2008, 3:59 PM
Send gmx-users mailing list submissions to
[email protected]
To subscribe or unsubscribe via the World Wide
Web, visit
http://www.gromacs.org/mailman/listinfo/gmx-users
or, via email, send a message with subject or body
'help' to
[EMAIL PROTECTED]
You can reach the person managing the list at
[EMAIL PROTECTED]
When replying, please edit your Subject line so it
is more
specific
than "Re: Contents of gmx-users
digest..."
Today's Topics:
1. Re: defination of cluster (Mark Abraham)
2. Box vector shifts number in x and y/z
dimension
(xuji)
3. How to calculate virial in gromacs-4.0?
(xuji)
4. RE: PME-user for electrostatics (Berk Hess)
5. Fatal error with grompp(with detail process)
(Jenny
Hsu)
----------------------------------------------------------------------
Message: 1
Date: Fri, 28 Nov 2008 12:24:52 +1100
From: Mark Abraham <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] defination of cluster
To: Discussion list for GROMACS users
<[email protected]>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1;
format=flowed
Q. Y. HUAN wrote:
Dear all,
I did the g_clustsize to get the number of
cluster
graph for my system. At the end of the simulation,
the total
number of cluster shown in the graph of my system
was 8.
Then I had a view in the trjectory and I found
that there
were total of 8 aggregated micelles and some free
monomer
(even it is a single molecule) which is same with
the result
shown in the graph.
ie 8 in the graph, 8 in the trajectory
My question is, how Gromacs define the
defination of
cluster? In my case, is it a free monomer (single
free
molecule) is also counted?
Did you start by reading g_clustsize -h?
Mark
------------------------------
Message: 2
Date: Fri, 28 Nov 2008 09:41:31 +0800
From: "xuji"<[EMAIL PROTECTED]>
Subject: [gmx-users] Box vector shifts number in x
and y/z
dimension
To: "[email protected]"
<[email protected]>
Message-ID:
<[EMAIL PROTECTED]>
Content-Type:
text/plain; charset="gb2312"
Hi all:
In gromacs all atoms are in the rectangular or
triclinic
unit-cell,
and in the codes using shifts with periodic
boundary
condition.
But why are there only single box vector shifts
required in
y and z dimensions
but 2 in x dimension ?
Thanks for any help in advance!
　　　　　　　　xuji
[EMAIL PROTECTED]
　　　　　　　　　　2008-11-28
------------------------------
Message: 3
Date: Fri, 28 Nov 2008 15:32:55 +0800
From: "xuji"<[EMAIL PROTECTED]>
Subject: [gmx-users] How to calculate virial in
gromacs-4.0?
To: "[email protected]"
<[email protected]>
Message-ID:
<[EMAIL PROTECTED]>
Content-Type:
text/plain; charset="gb2312"
Hi all
I want to do pressure coupling in my own program.
So These days I read associated codes in
Gromacs_4.0 and I
find that it
must sum the virial first. In Gromacs-3.3.3 you
use the
intramolecular shift(graph)
to sum the virial of the covalent bonds, but in
Gromacs-4.0
the graph variable seems to be NULL
when run the mdrun with domain decomposition. Is
it the
true?
And if it's true how do you sum the virial
with the
periodic boundary condition
in Gromacs_4.0 with domain decomposition? Can
someone
explain the way of summing
virial in Gromacs_4.0 in detail? Or can you
recommend some
resoures about summing the virial with
the periodic boundary condition?
Appreciate any help in advance!
Best
wishes!
　　　　　　　　xuji
[EMAIL PROTECTED]
　　　　　　　　　　2008-11-28
------------------------------
Message: 4
Date: Fri, 28 Nov 2008 08:56:16 +0100
From: Berk Hess <[EMAIL PROTECTED]>
Subject: RE: [gmx-users] PME-user for
electrostatics
To: Discussion list for GROMACS users
<[email protected]>
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain;
charset="iso-8859-1"
Hi,
PME splits the calculation in a Mesh part and a
direct
space part,
which is normally 1/r minus the mesh part. Note
that the
mesh part
also contributes below the cut-off.
If you want something else than 1/r at short range
(you always have 1/r beyond the cut-off)
than you can just give the short-range potential
you want,
mdrun takes care that it subtracts the short range
contribution of the mesh part.
Berk
Date: Thu, 27 Nov 2008 13:37:36 -0800
From: [EMAIL PROTECTED]
To: [email protected]
Subject: [gmx-users] PME-user for
electrostatics
hi,
i want to use a different function than the
Coulomb to
calculate the electrostatics
between charged ions. So i am thinking to user
the
PME-user option for the electrostatics.
The manual says for the PME-user
option"The PME
mesh contribution is subtracted from the user
table by
mdrun".
what that means? should i have to add the
short-range-potential (given by equation-4.33 in
the manual)
in the user table, because that will be
subtracted
with the mdrun?
please let me know, and thanks a lot for your
help
_______________________________________________
gmx-users mailing list
[email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests
to the
list. Use the
www interface or send it to
[EMAIL PROTECTED]
Can't post? Read
http://www.gromacs.org/mailing_lists/users.php
_________________________________________________________________
Express yourself instantly with MSN Messenger!
Download
today it's FREE!
http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/
-------------- next part --------------
An HTML attachment was scrubbed...
URL:
http://www.gromacs.org/pipermail/gmx-users/attachments/20081128/0f3a29db/attachment-0001.html
------------------------------
Message: 5
Date: Fri, 28 Nov 2008 15:58:41 +0800
From: "Jenny Hsu"
<[EMAIL PROTECTED]>
Subject: [gmx-users] Fatal error with grompp(with
detail
process)
To: "Discussion list for GROMACS users"
<[email protected]>
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain;
charset="iso-8859-1"
Hi all:
I have a problem with grompp
I want to making "POPC+protein" file
and I search the archieve and follow the process
1.run pdb2gmx for protein only
2.add below parameters into my topology file
#include "ffG53a6.itp"
#include "lipid.itp"
#include "popc.itp"
3.adjust the [ molecules ] section to list the
number and
type of my
components
4.run editconf and genbox
5.run grompp and it shows
Fatal error:
Atomtype CA not found
*Below is all information it shows*
*Can someone help me to solve this problem?*
*I am appreciate with that.*
*Thaks.*
:-) G R O M A C S (-:
Getting the Right Output Means no
Artefacts in
Calculating Stuff
:-) VERSION 4.0 (-:
Written by David van der Spoel, Erik
Lindahl, Berk
Hess, and others.
Copyright (c) 1991-2000, University of
Groningen,
The Netherlands.
Copyright (c) 2001-2008, The GROMACS
development team,
check out http://www.gromacs.org for
more
information.
This program is free software; you can
redistribute it and/or
modify it under the terms of the GNU
General
Public License
as published by the Free Software
Foundation;
either version 2
of the License, or (at your option)
any later
version.
:-) grompp (-:
Option Filename Type Description
------------------------------------------------------------
-f em.mdp Input, Opt! grompp input
file with MD
parameters
-po mdout.mdp Output grompp input file
with MD
parameters
-c 1UEO-nowater_water.gro Input
Structure file:
gro g96 pdb tpr
tpb
tpa
-r conf.gro Input, Opt. Structure file:
gro g96
pdb tpr tpb tpa
-rb conf.gro Input, Opt. Structure file:
gro g96
pdb tpr tpb tpa
-n index.ndx Input, Opt. Index file
-p 1UEO-nowater.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o 1UEO-nowater_em.tpr Output Run input
file: tpr
tpb tpa
-t traj.trr Input, Opt. Full precision
trajectory: trr trj cpt
-e ener.edr Input, Opt. Energy file: edr
ene
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and
quit
-nice int 0 Set the nicelevel
-[no]v bool yes Be loud and noisy
-time real -1 Take frame at or first
after
this time.
-[no]rmvsbds bool yes Remove constant bonded
interactions with virtual
sites
-maxwarn int 0 Number of allowed
warnings
during input
processing
-[no]zero bool no Set parameters for
bonded
interactions without
defaults to zero
instead of
generating an error
-[no]renum bool yes Renumber atomtypes and
minimize
number of
atomtypes
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Back Off! I just backed up mdout.mdp to
./#mdout.mdp.2#
checking input for internal consistency...
processing topology...
Opening library file
/usr/local/md/share/gromacs/top/ffG53a6.itp
Opening library file
/usr/local/md/share/gromacs/top/ffG53a6nb.itp
Opening library file
/usr/local/md/share/gromacs/top/ffG53a6bon.itp
Opening library file
/usr/local/md/share/gromacs/top/ff_dum.itp
WARNING 1 [file lipid.itp, line 14]:
Overriding atomtype LO
WARNING 2 [file lipid.itp, line 15]:
Overriding atomtype LOM
WARNING 3 [file lipid.itp, line 16]:
Overriding atomtype LNL
WARNING 4 [file lipid.itp, line 17]:
Overriding atomtype LC
WARNING 5 [file lipid.itp, line 18]:
Overriding atomtype LH1
WARNING 6 [file lipid.itp, line 19]:
Overriding atomtype LH2
WARNING 7 [file lipid.itp, line 20]:
Overriding atomtype LP
WARNING 8 [file lipid.itp, line 21]:
Overriding atomtype LOS
WARNING 9 [file lipid.itp, line 22]:
Overriding atomtype LP2
WARNING 10 [file lipid.itp, line 23]:
Overriding atomtype LP3
WARNING 11 [file lipid.itp, line 24]:
Overriding atomtype LC3
WARNING 12 [file lipid.itp, line 25]:
Overriding atomtype LC2
WARNING 13 [file lipid.itp, line 108]:
Overriding non-bonded parameters,
old: 0.00238804 3.38411e-06 new
LNL C 1 2.387718e-03 2.389594e-06
-------------------------------------------------------
Program grompp, VERSION 4.0
Source code file: toppush.c, line: 793
Fatal error:
Atomtype CA not found
--
Jenny Hsu, Biotechnology Dept.,
Ming Chuan University, Taiwan, R.O.C
-------------- next part --------------
An HTML attachment was scrubbed...
URL:
http://www.gromacs.org/pipermail/gmx-users/attachments/20081128/7cbaf26c/attachment.html
------------------------------
_______________________________________________
gmx-users mailing list
[email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/search
before posting!
End of gmx-users Digest, Vol 55, Issue 147
******************************************
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the
list. Use the
www interface or send it to
[EMAIL PROTECTED]
Can't post? Read
http://www.gromacs.org/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
------------------------------
Message: 4
Date: Fri, 28 Nov 2008 16:20:57 +0100
From: Berk Hess <[EMAIL PROTECTED]>
Subject: RE: [gmx-users] Box vector shifts number in x and
y/z
dimension
To: Discussion list for GROMACS users
<[email protected]>
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain; charset="iso-2022-jp"
Hi,
The b and c box vectors can be such that they both have as
x component
half the vector a x-length. Thus together they can cause a
shift of 1 full
x length and thus you might need 2 shifts along x.
Berk
Date: Fri, 28 Nov 2008 09:41:31 +0800
From: [EMAIL PROTECTED]
To: [email protected]
Subject: [gmx-users] Box vector shifts number in x and
y/z dimension
Hi all:
In gromacs all atoms are in the rectangular or
triclinic unit-cell,
and in the codes using shifts with periodic boundary
condition.
But why are there only single box vector shifts
required in y and z dimensions
but 2 in x dimension ?
Thanks for any help in advance!
$B!!!!!!!!!!!!!!!!(Bxuji
$B!!!!!!!!!!!!!!!!([EMAIL PROTECTED]
$B!!!!!!!!!!!!!!!!!!!!(B2008-11-28
_________________________________________________________________
Express yourself instantly with MSN Messenger! Download
today it's FREE!
http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/
-------------- next part --------------
An HTML attachment was scrubbed...
URL:
http://www.gromacs.org/pipermail/gmx-users/attachments/20081128/b82adbe7/attachment.html
------------------------------
_______________________________________________
gmx-users mailing list
[email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search
before posting!
End of gmx-users Digest, Vol 55, Issue 150
******************************************
