date:20120110


On 10/01/2012 7:13 PM, ahmet yıldırım wrote:

Dear users,

I created two different index files (A.ndx and B.ndx). I want to run 
the two files at the same time.

e.g.
g_hbond -f traj.xtc -s run.tpr -num A-B.xvg -n A.ndx -n B.ndx
where, I want to calculate the hydrogen bonds between A and B.
This command is giving the error as it expected. Gromacs tools do not 
support multi file input for index files from 
http://sbcb.bioch.ox.ac.uk/users/oliver/software/GromacsWrapper/html/gromacs/core/tools.html. 
Is this correct? If no, what should I do?


You can put your two groups in the same index file.

Run make_ndx and quit to see the format for index.ndx that it generates 
by default. You can do that too.


Mark
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Re:[gmx-users]-Snapshots

2012-01-10 Thread Rausch, Felix

 

Hi.

 

You will need a visualization program like VMD to get a 3D
representation of your system. After reading in the .gro file, you can
edit representation details and take pictures. 

 

Greetings,

Felix

 

Von: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] Im Auftrag von cuong nguyen
Gesendet: Dienstag, 10. Januar 2012 07:39
An: jalem...@vt.edu; Discussion list for GROMACS users
Betreff: Re: [gmx-users]-Snapshots

 

Thanks a lot Justin. I have just used trjconv -dump with the command
trjconv -s NVT_final2ns.tpr -f NVT_final2ns -o trjconv.gro -dump 1 to
extract a frame. However, I still do not know how to get the snapshot
like a 3D picture
data:image/png;base64,iVBORw0KGgoNSUhEUgAAAFkAAABUCAYAAADplZtxAAAKE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 .
Please help me!

Many thanks

Cuong Nguyen

2012/1/10 Justin A. Lemkul jalem...@vt.edu



cuong nguyen wrote:

Dear Users,

Please let me know if we can get snapshot from GROMACS. I am using
version 4.4.

 

The final configuration of any simulation is written to a coordinate
file by default.  You can extract any frame from your trajectory using
trjconv -dump.

-Justin

-- 


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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-- 

Nguyen Van Cuong

PhD student - Curtin University of Technology

Mobile: (+61) 452213981

 

 

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Re: [gmx-users] q question related to gromacsinstallation by cygwin


On 10/01/2012 5:45 PM, Dialing Pretty wrote:

Dear Mark,
If --disable-threads , how it will influence the function of GROMACS?


By preventing you from running mdrun with a separate execution thread in 
parallel on each physical processor that your machine has. If you need 
parallel functionality, compile with MPI enabled.


Secondly, for the webpage you introduced to me 
http://www.gromacs.org/Downloads/Installation_Instructions/Cygwin_HOWTO;, 
Edit your login files to source /usr/local/gromacs/bin/GMXRC (or 
manually add /usr/local/gromacs/man to the MANPATH and check that 
/usr/local/bin is in the PATH) is a little difficult to me. What is 
GMXRC? What is the login files? How to find the MANPATH? How do I 
know whther  /usr/local/bin is in the PATH is in the path? How can 
source /usr/local/gromacs/bin/GMXRC?


That page contains the strongly-worded advice to check the normal 
GROMACS installation instructions, which has a fuller discussion of this 
getting access to GROMACS issue. Please search the web for tutorials 
and discussion of how UNIX PATH environment variables function.


Mark


I am looking forward to getting a reply from you.
Dialing

*From:* Mark Abraham mark.abra...@anu.edu.au
*To:* Discussion list for GROMACS users gmx-users@gromacs.org
*Sent:* Tuesday, 10 January 2012 12:29 PM
*Subject:* Re: [gmx-users] q question related to gromacsinstallation 
by cygwin


On 10/01/2012 12:24 PM, Dialing Pretty wrote:

Dear All,

I have tried to install gromacs-4.5.5 by cygwin but I meet the 
following problems.


I am looking forward to getting your suggestions on how to solve the 
problem.


Dialing



$ make
Making all in include
make[1]: Entering directory `/cygdrive/d/GROMACS2/gromacs-4.5.5/include'
Making all in .
make[2]: Entering directory `/cygdrive/d/GROMACS2/gromacs-4.5.5/include'
make[2]: Nothing to be done for `all-am'.
make[2]: Leaving directory `/cygdrive/d/GROMACS2/gromacs-4.5.5/include'
Making all in types
make[2]: Entering directory 
`/cygdrive/d/GROMACS2/gromacs-4.5.5/include/types'

make[2]: *** No rule to make target `all'. Stop.
make[2]: Leaving directory 
`/cygdrive/d/GROMACS2/gromacs-4.5.5/include/types'

Makefile:479: recipe for target `all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/cygdrive/d/GROMACS2/gromacs-4.5.5/include'
Makefile:347: recipe for target `all-recursive' failed
make: *** [all-recursive] Error 1


The actual error occurred further up, so we cannot give specific help. 
Be sure you are following the instructions here 
http://www.gromacs.org/Downloads/Installation_Instructions/Cygwin_HOWTO, 
in particular --disable-threads.


Mark

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Re: [gmx-users] dynamic libraries and static libraries

2012-01-10 Thread Javier Cerezo


Hi

As far as I know, static libraries are linked during compilation, thus 
are part of your installation, while shared libraries are linked during 
execution. The latter lead to, somehow, more robust binaries, as once 
they are compiled they have (almost) no dependences, while the latter 
save memory (as indicated by the configure script), since you use 
libraries you already have in your system and you don't have to 
reinstall them again inside your program.


To enable/disable the use of shared libraries use --enable-shared (which 
is the default from gromacs 4.5.x) or --disable-shared along with the 
configure script.


Javier

El 10/01/12 07:38, Dialing Pretty escribió:


Dear All,
For GROMACS, what will be the difference by using static libraries and 
dynamic libraries? How can I install the static libraries and how can 
I install the dynamic libraries in GROMACS?

I am looking forward to getting your reply.
Dialing




--
Javier CEREZO BASTIDA
PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Tlf.(+34)868887434

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Re: [gmx-users] multi file input for index files

2012-01-10 Thread ahmet yıldırım

Hi,

But I want to calculate the hydrogen bonds between A and B groups. If I do
as you said, I will have calculated intra hydrogen bonds of a group AB
(merged A and B).

2012/1/10 Mark Abraham mark.abra...@anu.edu.au

On 10/01/2012 7:13 PM, ahmet yıldırım wrote:

Dear users,

I created two different index files (A.ndx and B.ndx). I want to run the
two files at the same time.
e.g.
g_hbond -f traj.xtc -s run.tpr -num A-B.xvg -n A.ndx -n B.ndx
where, I want to calculate the hydrogen bonds between A and B.
This command is giving the error as it expected. Gromacs tools do not
support multi file input for index files from
http://sbcb.bioch.ox.ac.uk/**users/oliver/software/**
GromacsWrapper/html/gromacs/**core/tools.htmlhttp://sbcb.bioch.ox.ac.uk/users/oliver/software/GromacsWrapper/html/gromacs/core/tools.html.
Is this correct? If no, what should I do?

You can put your two groups in the same index file.

Run make_ndx and quit to see the format for index.ndx that it generates by
default. You can do that too.

Mark
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Re: [gmx-users] dynamic libraries and static libraries


On 10/01/2012 5:38 PM, Dialing Pretty wrote:


Dear All,
For GROMACS, what will be the difference by using static libraries and 
dynamic libraries?


Static have fewer compatibility problems, but use rather more disk after 
installation.


How can I install the static libraries and how can I install the 
dynamic libraries in GROMACS?


See configure --help for the list of options, one of which pertains to 
shared libraries.


Mark
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Re: [gmx-users] multi file input for index files

On 10/01/2012 7:45 PM, ahmet y?ld?r?m wrote:

Hi,

But I want to calculate the hydrogen bonds between A and B groups. If
I do as you said, I will have calculated intra hydrogen bonds of a
group AB (merged A and B).

I didn't say to combine your groups. I said to put both group
definitions in the same file. Have you looked at the example I
suggested? Those groups are in the same file and yet distinct.

Mark

2012/1/10 Mark Abraham mark.abra...@anu.edu.au
mailto:mark.abra...@anu.edu.au

On 10/01/2012 7:13 PM, ahmet y?ld?r?m wrote:

Dear users,

http://sbcb.bioch.ox.ac.uk/users/oliver/software/GromacsWrapper/html/gromacs/core/tools.html.
Is this correct? If no, what should I do?

You can put your two groups in the same index file.

Run make_ndx and quit to see the format for index.ndx that it
generates by default. You can do that too.

Mark
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RE: [gmx-users] multi file input for index files

2012-01-10 Thread Marzinek, Jan

So as you can see Gromacs does not support multi file input :) Create one index 
file and specify there your two groups. Then g_hbond will ask you to choose two 
groups from this file.



Jan




===
Jan Marzinek
PhD Candidate
Centre for Process Systems Engineering
Department of Chemical Engineering
Imperial College London
South Kensington Campus
London SW7 2AZ
E: j.marzine...@imperial.ac.ukmailto:j.marzine...@imperial.ac.uk
M: +44(0)7411 640 552

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of ahmet yıldırım [ahmedo...@gmail.com]
Sent: Tuesday, January 10, 2012 8:13 AM
To: Discussion list for GROMACS users
Subject: [gmx-users] multi file input for index files

Dear users,

I created two different index files (A.ndx and B.ndx). I want to run the two 
files at the same time.
e.g.
g_hbond -f traj.xtc -s run.tpr -num A-B.xvg -n A.ndx -n B.ndx
where, I want to calculate the hydrogen bonds between A and B.
This command is giving the error as it expected. Gromacs tools do not support 
multi file input for index files from 
http://sbcb.bioch.ox.ac.uk/users/oliver/software/GromacsWrapper/html/gromacs/core/tools.html.
 Is this correct? If no, what should I do?

Thanks in advance
--
Ahmet Yıldırım

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Re: [gmx-users] multi file input for index files

2012-01-10 Thread ahmet yıldırım

Thanks Mark and Marzinek,

The Problem is solved:

g_hbond -f traj.xtc -s run.tpr -num AB.xvg -n AB.ndx

chain A

Found 1234 atoms with chain identifier A

19 chA : 1234 atoms

name 19 chainA

chain B

Found 1234 atoms with chain identifier B

20 chB : 1234 atoms

name 20 chainB

2012/1/10 Marzinek, Jan j.marzine...@imperial.ac.uk

So as you can see Gromacs does not support multi file input :) Create
one index file and specify there your two groups. Then g_hbond will ask you
to choose two groups from this file.

Jan

===
Jan Marzinek
PhD Candidate
Centre for Process Systems Engineering
Department of Chemical Engineering
Imperial College London
South Kensington Campus
London SW7 2AZ
E: j.marzine...@imperial.ac.uk
M: +44(0)7411 640 552
--
*From:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on
behalf of ahmet yıldırım [ahmedo...@gmail.com]
*Sent:* Tuesday, January 10, 2012 8:13 AM
*To:* Discussion list for GROMACS users
*Subject:* [gmx-users] multi file input for index files

Dear users,

I created two different index files (A.ndx and B.ndx). I want to run the
two files at the same time.
e.g.
g_hbond -f traj.xtc -s run.tpr -num A-B.xvg -n A.ndx -n B.ndx
where, I want to calculate the hydrogen bonds between A and B.
This command is giving the error as it expected. Gromacs tools do not
support multi file input for index files from
http://sbcb.bioch.ox.ac.uk/users/oliver/software/GromacsWrapper/html/gromacs/core/tools.html.
Is this correct? If no, what should I do?

Thanks in advance
--
Ahmet Yıldırım

Re: [gmx-users] Hello

Dear Gromacs users...

I am new to gromacs...

I have not understood this



In your shell configuration file (e.g. .bashrc for bash or .cshrc/.tcshrcfor
tcsh) you should use a command analogous to:

source /usr/local/gromacs/bin/GMXRC

near the end of that file.

can any one please tell me what is this..

nirmal

On Mon, Jan 9, 2012 at 1:48 PM, Mark Abraham mark.abra...@anu.edu.auwrote:

 On 9/01/2012 6:54 PM, Nirmal Prasad wrote:

 Dear Mark,

 Thanks for responding.

 I am new to Gromacs.

 I am working on Cytochrome P 450 proteins, these proteins contain HEME
 group.

 For MD run should I prepare separate protein and HEME group topologies
 and reconstruct protein-HEME complex.  Is this procedure is correct or
 not.


 A [moleculetype] cannot have covalent bonds with atoms outside itself. So
 whether your HEME group bonds covalently determines what can be found in a
 [moleculetype].

 Mark



 nirmal



 On 1/9/12, Mark Abrahammark.abra...@anu.edu.**aumark.abra...@anu.edu.au
  wrote:

 On 9/01/2012 6:42 PM, Nirmal Prasad wrote:

 Hello,

 I am working on Heme containing proteins, is it necessary to treat
 Heme group as Ligand.

 What do you mean by treating as a ligand?

 Mark
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Re: [gmx-users] Hello


On 10/01/2012 9:12 PM, Nirmal Prasad wrote:

Dear Gromacs users...

I am new to gromacs...

I have not understood this



In your shell configuration file (e.g. .bashrc for bash or 
.cshrc/.tcshrc for tcsh) you should use a command analogous to:


source /usr/local/gromacs/bin/GMXRC

near the end of that file.


can any one please tell me what is this..


I answered this question about two hours ago :) Consult the link that 
the page you quote suggests you read.


Mark
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Re: [gmx-users] RDF(PMF) and Umbrella sampling

2012-01-10 Thread Gavin Melaugh

Hi Justin

Again, many thanks for the reply.
So when the COM distance changes sign, what effect does that have on the
distribution of the COM distance about the mean value for that window
i.e. If say my ref dist in 0 nm and the umbrella sampling allows the
distance to sample distances say at 0.02 nm to -0.02nm. What happens to
negative values? Obviously they are not counted as negative in the
distribution or else it would be centred at zero/

Cheers

Gavin

Justin A. Lemkul wrote:

Gavin Melaugh wrote:
Hi Justin

Thanks very much. One last question. What do you mean when you say COM
reference distance is changing signs? I thought the COM distance was
the absolute distance between the two groups and therefore cannot be
negative?

The pull code deals in vectors. Signs can change. The use of
distance as a geometry is perhaps somewhat misleading.

-Justin

Cheers

Gavin

Dariush Mohammadyani wrote:
Hi Gavin,

A question arose for me: why did you consider the (rate = 0)?

Dariush

On Fri, Jan 6, 2012 at 11:47 AM, Gavin Melaugh gmelaug...@qub.ac.uk
mailto:gmelaug...@qub.ac.uk wrote:

Hi Justin

Just a quick clarification regarding my previous point. With
geometry =
distance, and pull_dim =Y Y Y . Is the pull_group sampling all
dimensions equally (or without prejudice) about pull_init ? And
iN your
first reply what did you mean about by straight pull ?

Cheers

Gavin

Justin A. Lemkul wrote:

Gavin Melaugh wrote:
Hi Justin

Thanks for the reply. I wanted my pulling to be free in all
directions, that is in the liquid state with no defined reaction
coordinate i.e not along a specific axis. This is why I used
geometry =
distance. Would you agree with this approach?

I suppose there is an argument that can be made for a more free
approach such as this one, but you're going to get the
artifact you
observed the instant your pull group moves past a zero COM
distance.
Whether or not this is a significant problem is something you'll
have
to determine.

-Justin

By free I mean. The absolute distance between the COG of the
ref group
and that of the pull group.

Cheers

Gavin

Justin A. Lemkul wrote:

Gavin Melaugh wrote:
Dear all

I have a query regarding umbrella sampling simulations that I
have
carried out to study a dynamical process of a guest inserting
into a
host. I always get get a wall tending off to infinity at or
just
before
the zero distance between the
two species.
The process I describe, for one system in particular, happens
readily
and I have compared the PMF from a non constrained simulation
(via the
RDF and reversible work theorem) and the same PMF from a
set of
umbrella sampling
simulations. They agree quite well but in the non constrained
simulation
I get a minimum practically at zero whereas for the umbrella
sampling
the minimum is shifted and there is an infinite wall close to
zero.
This
wall is not present from the reversible work theorem. Why the
infinite
wall? Why does the black histogram not centre around zero. Is
this an
artefact of the umbrella technique? Please see attached the
profile
from
the umbrella sampling technique, and the corresponding
histograms.

What's happening is the COM reference distance is changing
signs, so
you get an artifact. The distance geometry is relatively
inflexible
and is only suitable for straight pulls of continuously
increasing or
continuously decreasing COM distance. You should try using the
position geometry instead. There are some notes that you
may find
useful in my tutorial:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05a_pull_tips.html

-Justin

Here is an excerpt from one of the umbrella mdp files.

pull= umbrella
pull_geometry = distance
pull_dim = Y Y Y
pull_start = no
pull_ngroups = 1
pull_group0 = cage_1
pull_group1 = tail
pull_init1 = 0
pull_rate1 = 0.0
pull_k1 = 1
pull_nstxout = 150
pull_nstfout = 150

Cheers

Gavin

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[gmx-users] Energy Minimization

Dear Gmx Users,

I am setting up my simulations of carbon tube with protein. I solvated my
system, added ions and I would like to run EM of my system. My carbons of
the tube in MD will be restrained. In this case should I run EM of my
protein in water (and with ions) separately and the copy coordinates and
then process with NVT and NPT or run EM with restrained nanotubes of my
system directly?

Thank you,

Steven
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Re: [gmx-users] Energy Minimization


On 10/01/2012 9:54 PM, Steven Neumann wrote:

Dear Gmx Users,
I am setting up my simulations of carbon tube with protein. I solvated 
my system, added ions and I would like to run EM of my system. My 
carbons of the tube in MD will be restrained. In this case should I 
run EM of my protein in water (and with ions) separately and the copy 
coordinates and then process with NVT and NPT or run EM with 
restrained nanotubes of my system directly?


The former is less likely to have problems.

Mark
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Re: [gmx-users] Energy Minimization

Thank you. Should I also copy and paste coordinates of my ions or just my
protein?

Steven

On Tue, Jan 10, 2012 at 11:03 AM, Mark Abraham mark.abra...@anu.edu.auwrote:

 On 10/01/2012 9:54 PM, Steven Neumann wrote:

 Dear Gmx Users,
 I am setting up my simulations of carbon tube with protein. I solvated my
 system, added ions and I would like to run EM of my system. My carbons of
 the tube in MD will be restrained. In this case should I run EM of my
 protein in water (and with ions) separately and the copy coordinates and
 then process with NVT and NPT or run EM with restrained nanotubes of my
 system directly?


 The former is less likely to have problems.

 Mark
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Re: [gmx-users] multi file input for index files

2012-01-10 Thread Tsjerk Wassenaar

Hey,

In cases where you do end up with two index files, like resulting from
a script or so, you can also simply combine them by concatenation:

cat A.ndx B.ndx C.ndx

Of course you'll have to make sure that the group names are unique ;)

Cheers,

Tsjerk

2012/1/10 ahmet yıldırım ahmedo...@gmail.com:
Thanks Mark and Marzinek,

The Problem is solved:

g_hbond -f traj.xtc -s run.tpr -num AB.xvg -n AB.ndx

chain A

Found 1234 atoms with chain identifier A

19 chA : 1234 atoms

name 19 chainA

chain B

Found 1234 atoms with chain identifier B

20 chB : 1234 atoms

name 20 chainB

2012/1/10 Marzinek, Jan j.marzine...@imperial.ac.uk

So as you can see Gromacs does not support multi file input :) Create one
index file and specify there your two groups. Then g_hbond will ask you to
choose two groups from this file.

Jan

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on
behalf of ahmet yıldırım [ahmedo...@gmail.com]
Sent: Tuesday, January 10, 2012 8:13 AM
To: Discussion list for GROMACS users
Subject: [gmx-users] multi file input for index files

Dear users,

I created two different index files (A.ndx and B.ndx). I want to run the
two files at the same time.
e.g.
g_hbond -f traj.xtc -s run.tpr -num A-B.xvg -n A.ndx -n B.ndx
where, I want to calculate the hydrogen bonds between A and B.
This command is giving the error as it expected. Gromacs tools do not
support multi file input for index files from
http://sbcb.bioch.ox.ac.uk/users/oliver/software/GromacsWrapper/html/gromacs/core/tools.html.
Is this correct? If no, what should I do?

Thanks in advance
--
Ahmet Yıldırım

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Ahmet Yıldırım

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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] RDF(PMF) and Umbrella sampling

2012-01-10 Thread Thomas Schlesier

   pull_geometry = distance
   pull_dim = Y Y Y
   pull_start = no
   pull_ngroups = 1
   pull_group0 = cage_1
   pull_group1 = tail
   pull_init1 = 0
   pull_rate1 = 0.0
   pull_k1 = 1
   pull_nstxout = 150
   pull_nstfout = 150
 
 
   Cheers
 
   Gavin
 
 
 



 
 
 
 



 
 
 
 
 

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Kind Regards,
Dariush Mohammadyani
Department of Structural Biology
University of Pittsburgh School of Medicine
Biomedical Science Tower 3
3501 Fifth Avenue
Pittsburgh, PA 15261
USA









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Message: 3
Date: Tue, 10 Jan 2012 10:54:19 +
From: Steven Neumanns.neuman...@gmail.com
Subject: [gmx-users] Energy Minimization
To: Discussion list for GROMACS usersgmx-users@gromacs.org
Message-ID:
cakzjqqgcxr6pqjemepfjivu8+y_qn3bgmqm6jf3wksk48uv...@mail.gmail.com
Content-Type: text/plain; charset=iso-8859-1

Dear Gmx Users,

I am setting up my simulations of carbon tube with protein. I solvated my
system, added ions and I would like to run EM of my system. My carbons of
the tube in MD will be restrained. In this case should I run EM of my
protein in water (and with ions) separately and the copy coordinates and
then process with NVT and NPT or run EM with restrained nanotubes of my
system directly?

Thank you,

Steven
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Re: [gmx-users] Energy Minimization


On 10/01/2012 10:13 PM, Steven Neumann wrote:
Thank you. Should I also copy and paste coordinates of my ions or just 
my protein?




The randomly-placed ions will be immaterial for EM.

Mark
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Re: [gmx-users] Hello

I got this message pdb2gmx: command not found

but I installed gromacs..how to solve this error

nirmal

On Tue, Jan 10, 2012 at 3:48 PM, Mark Abraham mark.abra...@anu.edu.auwrote:

  On 10/01/2012 9:12 PM, Nirmal Prasad wrote:

 Dear Gromacs users...

 I am new to gromacs...

 I have not understood this

 

 In your shell configuration file (e.g. .bashrc for bash or .cshrc/.tcshrcfor
 tcsh) you should use a command analogous to:

 source /usr/local/gromacs/bin/GMXRC

 near the end of that file.
 
 can any one please tell me what is this..


 I answered this question about two hours ago :) Consult the link that the
 page you quote suggests you read.

 Mark

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Re: [gmx-users] RDF(PMF) and Umbrella sampling

2012-01-10 Thread Gavin Melaugh

 an artifact.  The distance geometry is relatively
  inflexible
and is only suitable for straight pulls of continuously
  increasing or
continuously decreasing COM distance.  You should try
 using the
position geometry instead.  There are some notes that you
  may find
useful in my tutorial:
  
  

 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05a_pull_tips.html


  
  
  
-Justin
  
Here is an excerpt from one of the umbrella mdp files.
  
pull= umbrella
pull_geometry = distance
pull_dim = Y Y Y
pull_start = no
pull_ngroups = 1
pull_group0 = cage_1
pull_group1 = tail
pull_init1 = 0
pull_rate1 = 0.0
pull_k1 = 1
pull_nstxout = 150
pull_nstfout = 150
  
  
Cheers
  
Gavin
  
  
  

 


  
  
  
  

 


  
  
  
  
  

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 -- 
 Kind Regards,
 Dariush Mohammadyani
 Department of Structural Biology
 University of Pittsburgh School of Medicine
 Biomedical Science Tower 3
 3501 Fifth Avenue
 Pittsburgh, PA 15261
 USA






 --

 Message: 3
 Date: Tue, 10 Jan 2012 10:54:19 +
 From: Steven Neumanns.neuman...@gmail.com
 Subject: [gmx-users] Energy Minimization
 To: Discussion list for GROMACS usersgmx-users@gromacs.org
 Message-ID:
 cakzjqqgcxr6pqjemepfjivu8+y_qn3bgmqm6jf3wksk48uv...@mail.gmail.com
 Content-Type: text/plain; charset=iso-8859-1

 Dear Gmx Users,

 I am setting up my simulations of carbon tube with protein. I
 solvated my
 system, added ions and I would like to run EM of my system. My
 carbons of
 the tube in MD will be restrained. In this case should I run EM of my
 protein in water (and with ions) separately and the copy coordinates and
 then process with NVT and NPT or run EM with restrained nanotubes of my
 system directly?

 Thank you,

 Steven
 -- next part --
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Re: [gmx-users] Energy Minimization

Thank you. Imagine I would like to put ligands in further simulations.
Should I then copy coordinates of my ligands in smaller box (not to overlap
my tube) and then copy both coordinates of ions and ligands plus protein?

On Tue, Jan 10, 2012 at 11:31 AM, Mark Abraham mark.abra...@anu.edu.auwrote:

 On 10/01/2012 10:13 PM, Steven Neumann wrote:

 Thank you. Should I also copy and paste coordinates of my ions or just my
 protein?


 The randomly-placed ions will be immaterial for EM.


 Mark
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[gmx-users] homodimer simulation

2012-01-10 Thread Kavyashree M

Dear user,

I simulated a homodimer of 238aa each with oplsaa forcefield
using gromacs-4.5.3. But while calculating the rmsf plot I got a
plot in which starting and ending residue were connected by a
straight line along with the actual rmsf plot. Also the two rmsf
plots that it gave were slightly different from each other in few
regions. I was expecting similar rmsf for both the monomers.
I checked the pdb file generated after md run, it did not have chain
ID but two chains were present.

Kindly let me know what is wrong with rmsf? Or what is wrong with
simulation.

Thanking you
With Regards
avya
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[gmx-users] Mixture of H2O and D2O

2012-01-10 Thread Hernan Ahumada

Dear gmx users

I am trying to run a MD with a mixture of D2O and H2O. I defined a new itp
spcdeut.itp for heavy water and the usualy spc.itp for normal water. when I try
to run grompp appear this error:

The [molecules] section of your topology specifies more than one block of
a [moleculetype] with a [settles] block. Only one such is allowed. If you
are trying to partition your solvent into different *groups* (e.g. for
freezing, T-coupling, etc.) then you are using the wrong approach. Index
files specify groups. Otherwise, you may wish to change the least-used
block of molecules with SETTLE constraints into 3 normal constraints.

Any of you can help me with te meaning of this error? because if I define
=-DFLEXIBLE I solve the error.

Thank you very much



This message was sent using IMP, the Internet Messaging Program.
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Re: [gmx-users] Hello

On 10/01/2012 10:37 PM, Nirmal Prasad wrote:

I got this message pdb2gmx: command not found

but I installed gromacs..how to solve this error

You need a functional PATH. See
http://www.gromacs.org/Downloads/Installation_Instructions#Getting_access_to_GROMACS_after_installation.

Mark

nirmal

On Tue, Jan 10, 2012 at 3:48 PM, Mark Abraham mark.abra...@anu.edu.au
mailto:mark.abra...@anu.edu.au wrote:

On 10/01/2012 9:12 PM, Nirmal Prasad wrote:

Dear Gromacs users...

I am new to gromacs...

I have not understood this

In your shell configuration file (e.g. .bashrc for bash or
.cshrc/.tcshrc for tcsh) you should use a command analogous to:

source /usr/local/gromacs/bin/GMXRC

near the end of that file.

can any one please tell me what is this..

I answered this question about two hours ago :) Consult the link
that the page you quote suggests you read.

Mark

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Re: [gmx-users] Energy Minimization


On 10/01/2012 10:46 PM, Steven Neumann wrote:
Thank you. Imagine I would like to put ligands in further simulations. 
Should I then copy coordinates of my ligands in smaller box (not to 
overlap my tube) and then copy both coordinates of ions and ligands 
plus protein?


Any way you want to construct your non-overlapping non-solvent non-ion 
molecules is fine. Previous EM of each is wise, but not necessarily 
required - vacuo EM is probably fine. Then solvate, then use genion, 
then EM the whole system. Copying ions from earlier calculations is a 
good way to generate atomic clashes, which is a high price to pay for 
randomly-placed ions that are different from those generated as above.


Mark



On Tue, Jan 10, 2012 at 11:31 AM, Mark Abraham 
mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote:


On 10/01/2012 10:13 PM, Steven Neumann wrote:

Thank you. Should I also copy and paste coordinates of my ions
or just my protein?


The randomly-placed ions will be immaterial for EM.


Mark
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Re: [gmx-users] Mixture of H2O and D2O


On 10/01/2012 10:35 PM, Hernan Ahumada wrote:

Dear gmx users

I am trying to run a MD with a mixture of D2O and H2O. I defined a new itp
spcdeut.itp for heavy water and the usualy spc.itp for normal water. when I try
to run grompp appear this error:

The [molecules] section of your topology specifies more than one block of
a [moleculetype] with a [settles] block. Only one such is allowed. If you
are trying to partition your solvent into different *groups* (e.g. for
freezing, T-coupling, etc.) then you are using the wrong approach. Index
files specify groups. Otherwise, you may wish to change the least-used
block of molecules with SETTLE constraints into 3 normal constraints.


You need to follow the advice in the last sentence because of the first 
sentence.



Any of you can help me with te meaning of this error? because if I define
=-DFLEXIBLE I solve the error.


... because -DFLEXIBLE removes constraints, the SETTLE constraints don't 
exist, so they can't clash. You'd also be using a different water model 
than was parametrized. This can be OK for overcoming atom placement 
issues during setup, but is not useful for simulations.


Mark
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[gmx-users] About g_msd. I want to plot the curve from 0.01ps.

2012-01-10 Thread Kiwoong Kim

Hi

I have been learning how to use gromacs owing to your advice.

I have simple question on g_msd.
I tried to plot MSD curve using g_msd. I want to deeply investigate the MSD
curve from 0.01ps to the last of simulation (my case, 1ns).

However, g_msd always produce the MSD curve starting from 1ps.
How can I adjust the instance of starting time of MSD curve (for example,
0.01ps - 1ns)??

please help me.

Have a nice day!
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Re: [gmx-users] Hello

Dear Mark,

Thank you very much..now its working

nirmal

On Tue, Jan 10, 2012 at 5:31 PM, Mark Abraham mark.abra...@anu.edu.auwrote:

On 10/01/2012 10:37 PM, Nirmal Prasad wrote:

I got this message pdb2gmx: command not found

but I installed gromacs..how to solve this error

You need a functional PATH. See
http://www.gromacs.org/Downloads/Installation_Instructions#Getting_access_to_GROMACS_after_installation
.

Mark

nirmal

On Tue, Jan 10, 2012 at 3:48 PM, Mark Abraham mark.abra...@anu.edu.auwrote:

On 10/01/2012 9:12 PM, Nirmal Prasad wrote:

Dear Gromacs users...

I am new to gromacs...

I have not understood this

In your shell configuration file (e.g. .bashrc for bash or .cshrc/.tcshrcfor
tcsh) you should use a command analogous to:

source /usr/local/gromacs/bin/GMXRC

near the end of that file.

can any one please tell me what is this..

I answered this question about two hours ago :) Consult the link that
the page you quote suggests you read.

Mark

Re: [gmx-users] RDF(PMF) and Umbrella sampling

2012-01-10 Thread Thomas Schlesier

The histograms are really crowded, it would be better to plot only the 
black one and probably the red one, to see the it better.


Two ideas which can probably solve the problem (ok, both assume, that
the host has a certain shape).

You said you investigate guest-insertion to a host. I would think that
the guest molecule can't bind from all directions to the host.
If the host is 'U' shaped then, the guest can come only from above.

Idea 1:
Take some atoms at the lower part from 'U' as the reference. So you do
not run into the problem with with a zero ref-distance.
Bad thing is, that you would start from all over again.

Idea 2: we make some tricks to get negative distances. I think the big 
problem is that from pull_geometry=distance, you get always positive 
distances
(really, only a idea, WHAM could make problems, i don't really know how 
WHAM and the GROMACS implementation of it work):

Instead of using pull_geometry=distance, use pull_geometry=position.
Define a plane at zero ref-distance, which is roughly orthogonal to the
path which the guest can enter.
In my example 'U-'  -  would be the plane.
From the pullx.xvg you can calculate the pull-ref distance (which is
always positive). Then you can add a sign to the distances, depending if 
the guest is above or below the plane. (Probably it is better to take 
only the part of the pull-ref distance which is orthogonal to the plane. 
Then you should also modify the forces in the same way.)

From this distances you can also calculate pullf.xvg.
Now you must create a *.tpr for this windows with 
pull_geometry=distance, instead of use pull_geometry=position (WHAM 
doesn't like position, as far as i know).
Now start WHAM and pray that it will work. All we have done is, that we 
have now negative distances in pullx.xvg. I don't know if the fact that 
we now have negative numbers makes any problem for WHAM (from the *.tpr 
we would expect that we have only positive numbers).


Wish you luck.
greetings
thomas






Date: Tue, 10 Jan 2012 10:47:43 +
From: Gavin Melaughgmelaug...@qub.ac.uk
Subject: Re: [gmx-users] RDF(PMF) and Umbrella sampling
To: Discussion list for GROMACS usersgmx-users@gromacs.org
Message-ID:4f0c174f.2050...@qub.ac.uk
Content-Type: text/plain; charset=ISO-8859-1

Hi Justin

Again, many thanks for the reply.
So when the COM distance changes sign, what effect does that have on the
distribution of the COM distance about the mean value for that window
i.e. If say my ref dist in 0 nm and the umbrella sampling allows the
distance to sample distances say at 0.02 nm to -0.02nm. What happens to
negative values? Obviously they are not counted as negative in the
distribution or else it would be centred at zero/

Cheers

Gavin

Justin A. Lemkul wrote:



Gavin Melaugh wrote:

Hi Justin

Thanks very much. One last question. What do you mean when you say COM
reference distance is changing signs? I thought  the COM distance was
the absolute distance between the two groups and therefore cannot be
negative?



The pull code deals in vectors.  Signs can change.  The use of
distance as a geometry is perhaps somewhat misleading.

-Justin


Cheers

Gavin

Dariush Mohammadyani wrote:

Hi Gavin,

A question arose for me: why did you consider the (rate = 0)?

Dariush


On Fri, Jan 6, 2012 at 11:47 AM, Gavin Melaughgmelaug...@qub.ac.uk
mailto:gmelaug...@qub.ac.uk  wrote:

 Hi Justin

 Just a quick clarification regarding my previous point. With
 geometry =
 distance, and pull_dim =Y Y Y . Is the pull_group sampling all
 dimensions equally (or without prejudice) about pull_init ?  And
 iN your
 first reply what did you mean about by straight pull ?

 Cheers

 Gavin

 Justin A. Lemkul wrote:
 
 
   Gavin Melaugh wrote:
   Hi Justin
 
   Thanks for the reply. I wanted my pulling to be free in all
   directions, that is in the liquid state with no defined reaction
   coordinate i.e not along a specific axis. This is why I used
 geometry =
   distance. Would you agree with this approach?
 
   I suppose there is an argument that can be made for a more free
   approach such as this one, but you're going to get the
artifact you
   observed the instant your pull group moves past a zero COM
distance.
   Whether or not this is a significant problem is something you'll
 have
   to determine.
 
   -Justin
 
   By free I mean. The absolute distance between the COG of the
 ref group
   and that of the pull group.
 
   Cheers
 
   Gavin
 
   Justin A. Lemkul wrote:
 
   Gavin Melaugh wrote:
   Dear all
 
   I have a query regarding umbrella sampling simulations that I
 have
   carried out to study a dynamical process of a guest inserting
 into a
   host. I always get get a wall tending off to infinity at or
just
   before
   the zero distance between the
   two species.

Re: [gmx-users] problem with gromacs

2012-01-10 Thread Sylwia Chmielewska

Hello,
Thanks for the advice. For one moment everything was ok, but at some point 
appeared an error.

$ cd gromacs-4.5.5
./configure --disable-threads
make
.libs/xlate.o:xlate.c:(.text+0x774): undefined reference to `_save_free'
.libs/xlate.o:xlate.c:(.text+0x7a0): undefined reference to `_save_free'
.libs/xlate.o:xlate.c:(.text+0x7da): undefined reference to `_save_free'
.libs/xlate.o:xlate.c:(.text+0x801): more undefined references to `_save_free' 
follow
.libs/xlate.o:xlate.c:(.text+0x9d5): undefined reference to 
`_gmx_residuetype_is_rna'
.libs/xlate.o:xlate.c:(.text+0xa9b): undefined reference to `_put_symtab'
.libs/xlate.o:xlate.c:(.text+0xb3a): undefined reference to `_save_free'
.libs/xlate.o:xlate.c:(.text+0xba6): undefined reference to `_save_free'
.libs/xlate.o:xlate.c:(.text+0xc0d): undefined reference to `_save_free'
.libs/xlate.o:xlate.c:(.text+0xc6d): undefined reference to `_save_free'
.libs/xlate.o:xlate.c:(.text+0xc99): undefined reference to `_save_free'
collect2: ld returned 1 exit status
Makefile:459: recipe for target `libgmxpreprocess.la' failed
make[3]: *** [libgmxpreprocess.la] Error 1
make[3]: Leaving directory `/home/Sylwia/gromacs-4.5.5/src/kernel'
Makefile:302: recipe for target `all-recursive' failed
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/Sylwia/gromacs-4.5.5/src'
Makefile:238: recipe for target `all' failed
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/Sylwia/gromacs-4.5.5/src'
Makefile:347: recipe for target `all-recursive' failed
make: *** [all-recursive] Error 1

What have I done now?

Sylwia Chmielewska

- Oryginalna wiadomość -
Od: Mark Abraham mark.abra...@anu.edu.au
Do: Discussion list for GROMACS users gmx-users@gromacs.org
Wysłane: niedziela, 8 styczeń 2012 23:37:42
Temat: Re: [gmx-users] problem with gromacs


On 9/01/2012 3:44 AM, Sylwia Chmielewska wrote:

Hello
Folder with the program GROMACS save in a folder cygwin / home / Sylwia.
then:
$ cd gromacs-4.5.5

./configure --enable-sse --enable-float
no errors occurred only at the end:

configure: WARNING: unrecognized options: - enable-sse
You'll note that 
http://www.gromacs.org/Downloads/Installation_Instructions/Cygwin_HOWTO does 
not recommend --enable-sse for this part of the procedure.



make
no errors occurred only at the end:

numa_malloc.c:117:73: error: expected ‘)’ before ‘Processor’
numa_malloc.c:118:78: error: expected ‘)’ before ‘ProcNumber’
numa_malloc.c:121:45: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ 
before ‘smalloc_GetNumaProcessorNodeEx’
numa_malloc.c:122:45: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ 
before ‘smalloc_GetCurrentProcessorNumberEx’
numa_malloc.c: In function ‘InitNumaHeapSupport’:
numa_malloc.c:151:5: error: ‘smalloc_GetCurrentProcessorNumberEx’ undeclared 
(first use in this function)
numa_malloc.c:151:5: note: each undeclared identifier is reported only once for 
each function it appears in
numa_malloc.c:151:44: error: ‘func_GetCurrentProcessorNumberEx_t’ undeclared 
(first use in this function)
numa_malloc.c:151:79: error: expected ‘;’ before ‘GetProcAddress’
numa_malloc.c:152:5: error: ‘smalloc_GetNumaProcessorNodeEx’ undeclared (first 
use in this function)
numa_malloc.c:152:39: error: ‘func_GetNumaProcessorNodeEx_t’ undeclared (first 
use in this function)
numa_malloc.c:152:69: error: expected ‘;’ before ‘GetProcAddress’
numa_malloc.c: In function ‘ReturnHeapHandle’:
numa_malloc.c:246:5: error: ‘PROCESSOR_NUMBER’ undeclared (first use in this 
function)
numa_malloc.c:246:22: error: expected ‘;’ before ‘CurrentProcessorNumber’
numa_malloc.c:285:5: warning: implicit declaration of function 
‘smalloc_GetCurrentProcessorNumberEx’
numa_malloc.c:285:42: error: ‘CurrentProcessorNumber’ undeclared (first use in 
this function)
numa_malloc.c:287:5: warning: implicit declaration of function 
‘smalloc_GetNumaProcessorNodeEx’
numa_malloc.c:324:9: warning: implicit declaration of function 
‘HeapSetInformation’
Makefile:332: recipe for target `numa_malloc.lo' failed
make[4]: *** [numa_malloc.lo] Error 1
make[4]: Leaving directory `/home/Sylwia/gromacs-4.5.5/src/gmxlib/thread_mpi'
Makefile:599: recipe for target `all-recursive' failed
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory `/home/Sylwia/gromacs-4.5.5/src/gmxlib'
Makefile:302: recipe for target `all-recursive' failed
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/Sylwia/gromacs-4.5.5/src'
Makefile:238: recipe for target `all' failed
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/Sylwia/gromacs-4.5.5/src'
Makefile:347: recipe for target `all-recursive' failed
make: *** [all-recursive] Error 1

make install
Once something goes wrong, trying to press forward is normally fruitless.

There's a bug with threading that shows up with version 4.5.5 on Cygwin. Use 
configure --disable-threads (and whatever else you need to use).

Mark



the same thing:

cc -DHAVE_CONFIG_H -I. -I../../../src

[gmx-users] how to model linear rigid molecules (CO2)

2012-01-10 Thread Kiwoong Kim

Hi,

I need to model linear rigid molecules, CO2.
I understood that the virtual site have to be introduced to model CO2
like below way.

[ atomtypes ]
;   type  masschargeptype   c6c12
D1 22.0049750.   A 0.  0.
D2  22.004975   0.   A 0.  0.
C_CO 0.000  0.5406   V 0.  0.
O_CO 0.000 -0.2703   V 0.29847   1.10765301

[ moleculetype]
.
.
.
etc.

However, my question is that I don't know how to give coordinates of
dummy particle to the initial coordinate file(i.e., my pdb file) which
already has coordinates of C, O, and O but not dummy particle yet.
My simulation case is not standard, so pdb2gmx is not working. I have
to build each file by hand.
Thx.
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Re: [gmx-users] problem with gromacs


On 11/01/2012 12:32 AM, Sylwia Chmielewska wrote:

Hello,
Thanks for the advice. For one moment everything was ok, but at some point 
appeared an error.


Use make distclean before configure if you have already configured and 
built and need to change stuff. Else things can get confused sometimes.


Mark



$ cd gromacs-4.5.5
./configure --disable-threads
make
.libs/xlate.o:xlate.c:(.text+0x774): undefined reference to `_save_free'
.libs/xlate.o:xlate.c:(.text+0x7a0): undefined reference to `_save_free'
.libs/xlate.o:xlate.c:(.text+0x7da): undefined reference to `_save_free'
.libs/xlate.o:xlate.c:(.text+0x801): more undefined references to `_save_free' 
follow
.libs/xlate.o:xlate.c:(.text+0x9d5): undefined reference to 
`_gmx_residuetype_is_rna'
.libs/xlate.o:xlate.c:(.text+0xa9b): undefined reference to `_put_symtab'
.libs/xlate.o:xlate.c:(.text+0xb3a): undefined reference to `_save_free'
.libs/xlate.o:xlate.c:(.text+0xba6): undefined reference to `_save_free'
.libs/xlate.o:xlate.c:(.text+0xc0d): undefined reference to `_save_free'
.libs/xlate.o:xlate.c:(.text+0xc6d): undefined reference to `_save_free'
.libs/xlate.o:xlate.c:(.text+0xc99): undefined reference to `_save_free'
collect2: ld returned 1 exit status
Makefile:459: recipe for target `libgmxpreprocess.la' failed
make[3]: *** [libgmxpreprocess.la] Error 1
make[3]: Leaving directory `/home/Sylwia/gromacs-4.5.5/src/kernel'
Makefile:302: recipe for target `all-recursive' failed
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/Sylwia/gromacs-4.5.5/src'
Makefile:238: recipe for target `all' failed
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/Sylwia/gromacs-4.5.5/src'
Makefile:347: recipe for target `all-recursive' failed
make: *** [all-recursive] Error 1

What have I done now?

Sylwia Chmielewska

- Oryginalna wiadomość -
Od: Mark Abrahammark.abra...@anu.edu.au
Do: Discussion list for GROMACS usersgmx-users@gromacs.org
Wysłane: niedziela, 8 styczeń 2012 23:37:42
Temat: Re: [gmx-users] problem with gromacs


On 9/01/2012 3:44 AM, Sylwia Chmielewska wrote:

Hello
Folder with the program GROMACS save in a folder cygwin / home / Sylwia.
then:
$ cd gromacs-4.5.5

./configure --enable-sse --enable-float
no errors occurred only at the end:

configure: WARNING: unrecognized options: - enable-sse
You'll note that 
http://www.gromacs.org/Downloads/Installation_Instructions/Cygwin_HOWTO does 
not recommend --enable-sse for this part of the procedure.



make
no errors occurred only at the end:

numa_malloc.c:117:73: error: expected ‘)’ before ‘Processor’
numa_malloc.c:118:78: error: expected ‘)’ before ‘ProcNumber’
numa_malloc.c:121:45: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ 
before ‘smalloc_GetNumaProcessorNodeEx’
numa_malloc.c:122:45: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ 
before ‘smalloc_GetCurrentProcessorNumberEx’
numa_malloc.c: In function ‘InitNumaHeapSupport’:
numa_malloc.c:151:5: error: ‘smalloc_GetCurrentProcessorNumberEx’ undeclared 
(first use in this function)
numa_malloc.c:151:5: note: each undeclared identifier is reported only once for 
each function it appears in
numa_malloc.c:151:44: error: ‘func_GetCurrentProcessorNumberEx_t’ undeclared 
(first use in this function)
numa_malloc.c:151:79: error: expected ‘;’ before ‘GetProcAddress’
numa_malloc.c:152:5: error: ‘smalloc_GetNumaProcessorNodeEx’ undeclared (first 
use in this function)
numa_malloc.c:152:39: error: ‘func_GetNumaProcessorNodeEx_t’ undeclared (first 
use in this function)
numa_malloc.c:152:69: error: expected ‘;’ before ‘GetProcAddress’
numa_malloc.c: In function ‘ReturnHeapHandle’:
numa_malloc.c:246:5: error: ‘PROCESSOR_NUMBER’ undeclared (first use in this 
function)
numa_malloc.c:246:22: error: expected ‘;’ before ‘CurrentProcessorNumber’
numa_malloc.c:285:5: warning: implicit declaration of function 
‘smalloc_GetCurrentProcessorNumberEx’
numa_malloc.c:285:42: error: ‘CurrentProcessorNumber’ undeclared (first use in 
this function)
numa_malloc.c:287:5: warning: implicit declaration of function 
‘smalloc_GetNumaProcessorNodeEx’
numa_malloc.c:324:9: warning: implicit declaration of function 
‘HeapSetInformation’
Makefile:332: recipe for target `numa_malloc.lo' failed
make[4]: *** [numa_malloc.lo] Error 1
make[4]: Leaving directory `/home/Sylwia/gromacs-4.5.5/src/gmxlib/thread_mpi'
Makefile:599: recipe for target `all-recursive' failed
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory `/home/Sylwia/gromacs-4.5.5/src/gmxlib'
Makefile:302: recipe for target `all-recursive' failed
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/Sylwia/gromacs-4.5.5/src'
Makefile:238: recipe for target `all' failed
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/Sylwia/gromacs-4.5.5/src'
Makefile:347: recipe for target `all-recursive' failed
make: *** [all-recursive] Error 1

make install
Once something goes wrong, trying to press forward is normally fruitless.

There's a bug

Re: [gmx-users] About g_msd. I want to plot the curve from 0.01ps.


On 10/01/2012 11:21 PM, Kiwoong Kim wrote:

Hi

I have been learning how to use gromacs owing to your advice.

I have simple question on g_msd.
I tried to plot MSD curve using g_msd. I want to deeply investigate 
the MSD curve from 0.01ps to the last of simulation (my case, 1ns).


However, g_msd always produce the MSD curve starting from 1ps.
How can I adjust the instance of starting time of MSD curve (for 
example, 0.01ps - 1ns)??




It can't analyze more frames than exist in your trajectory file, which 
you controlled with your .mdp file when you ran the simulation. See what 
gmxcheck has to say about your trajectory file.


Mark
--
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Re: [gmx-users] About g_msd. I want to plot the curve from 0.01ps.




Kiwoong Kim wrote:

Hi

I have been learning how to use gromacs owing to your advice.

I have simple question on g_msd.
I tried to plot MSD curve using g_msd. I want to deeply investigate the 
MSD curve from 0.01ps to the last of simulation (my case, 1ns).


However, g_msd always produce the MSD curve starting from 1ps. 
How can I adjust the instance of starting time of MSD curve (for 
example, 0.01ps - 1ns)??




Please read g_msd -h, with particular attention to the section on -beginfit and 
-endfit.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Regarding NVT NPT ensemble

2012-01-10 Thread ajani haresh

Dear Sir,

I am new user in Gromacs. I am using Gromacs  for protein-ligand complex.
If I am not wrong MD simulation have three part.
1. Energy Minimization
2. Equilibration  phase
3. Production phase

After EM minimization we run Equilibration using (NVT  NPT ensemble).

I have little sily question in MD simulation.

1. In Protein-Ligand complex compulsory we have to run NVT  NPT ensemble ?

2 shall we run without NPT ensemble MD production phase ?

3. If we use both ensemble in production phase system might be NVPT like
during production phase.

4. If we run only without NPT ensemble during production phase its affect
MD simulation ?


Thanks and Regards,




-- 
-
Haresh Ajani
09925522578
-- 
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Re: [gmx-users] Regarding NVT NPT ensemble


On 11/01/2012 1:14 AM, ajani haresh wrote:

Dear Sir,

I am new user in Gromacs. I am using Gromacs  for protein-ligand complex.
If I am not wrong MD simulation have three part.
1. Energy Minimization
2. Equilibration  phase
3. Production phase

After EM minimization we run Equilibration using (NVT  NPT ensemble).

I have little sily question in MD simulation.

1. In Protein-Ligand complex compulsory we have to run NVT  NPT 
ensemble ?


There's nothing that is required, but the advice here is fairly sound: 
http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation. 
If your density is already correct, then NPT equilibration before NVT 
simulation doesn't help anything.



2 shall we run without NPT ensemble MD production phase ?


Depends what you want to observe.

3. If we use both ensemble in production phase system might be NVPT 
like during production phase.


You cannot have an NVPT ensemble, i.e one with constant volume that is 
coupled to a pressure bath.


4. If we run only without NPT ensemble during production phase its 
affect MD simulation ?


Yes. Only you can assess the impact on your objectives.

Mark
--
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[gmx-users] Re: gmx-users Digest, Vol 93, Issue 52

2012-01-10 Thread ajani haresh

Thanks Sir,

But I have one more question.

If I run first NVT then NPT ensemble. So we get output file from NPT
ensemble.

NPT ensemble output we will use into production phase.

Means they also take parameter from NVT ensemble.

Thanks in advance


 Message: 6
 Date: Wed, 11 Jan 2012 01:20:20 +1100
 From: Mark Abraham mark.abra...@anu.edu.au
 Subject: Re: [gmx-users] Regarding NVT  NPT ensemble
 To: Discussion list for GROMACS users gmx-users@gromacs.org
 Message-ID: 4f0c4924.5020...@anu.edu.au
 Content-Type: text/plain; charset=ISO-8859-1; format=flowed

 On 11/01/2012 1:14 AM, ajani haresh wrote:
  Dear Sir,
 
  I am new user in Gromacs. I am using Gromacs  for protein-ligand complex.
  If I am not wrong MD simulation have three part.
  1. Energy Minimization
  2. Equilibration  phase
  3. Production phase
 
  After EM minimization we run Equilibration using (NVT  NPT ensemble).
 
  I have little sily question in MD simulation.
 
  1. In Protein-Ligand complex compulsory we have to run NVT  NPT
  ensemble ?

 There's nothing that is required, but the advice here is fairly sound:
 http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation
 .
 If your density is already correct, then NPT equilibration before NVT
 simulation doesn't help anything.

  2 shall we run without NPT ensemble MD production phase ?

 Depends what you want to observe.

  3. If we use both ensemble in production phase system might be NVPT
  like during production phase.

 You cannot have an NVPT ensemble, i.e one with constant volume that is
 coupled to a pressure bath.

  4. If we run only without NPT ensemble during production phase its
  affect MD simulation ?

 Yes. Only you can assess the impact on your objectives.

 Mark


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09925522578
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Re: [gmx-users] Regarding NVT NPT ensemble




ajani haresh wrote:

Thanks Sir,

But I have one more question.

If I run first NVT then NPT ensemble. So we get output file from NPT 
ensemble.


NPT ensemble output we will use into production phase.

Means they also take parameter from NVT ensemble.



The two ensembles work in concert to produce the final ensemble that is used 
during data collection.  NVT relaxes the system such that the temperature is 
stable and you are obtaining values in the correct distribution.  You pass that 
output to NPT to preserve previous state information and begin a new ensemble, 
which now maintains temperature and stabilizes the pressure.


For some systems, you could probably bypass NVT and go straight to NPT 
equilibration; the exact procedure depends on how robust your system is.  The 
progression of NVT - NPT - data collection is common and intuitive, by not 
necessarily the only way to proceed.


-Justin


Thanks in advance
 


Message: 6
Date: Wed, 11 Jan 2012 01:20:20 +1100
From: Mark Abraham mark.abra...@anu.edu.au
mailto:mark.abra...@anu.edu.au
Subject: Re: [gmx-users] Regarding NVT  NPT ensemble
To: Discussion list for GROMACS users gmx-users@gromacs.org
mailto:gmx-users@gromacs.org
Message-ID: 4f0c4924.5020...@anu.edu.au
mailto:4f0c4924.5020...@anu.edu.au
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

On 11/01/2012 1:14 AM, ajani haresh wrote:
  Dear Sir,
 
  I am new user in Gromacs. I am using Gromacs  for protein-ligand
complex.
  If I am not wrong MD simulation have three part.
  1. Energy Minimization
  2. Equilibration  phase
  3. Production phase
 
  After EM minimization we run Equilibration using (NVT  NPT
ensemble).
 
  I have little sily question in MD simulation.
 
  1. In Protein-Ligand complex compulsory we have to run NVT  NPT
  ensemble ?

There's nothing that is required, but the advice here is fairly sound:
http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation.
If your density is already correct, then NPT equilibration before NVT
simulation doesn't help anything.

  2 shall we run without NPT ensemble MD production phase ?

Depends what you want to observe.

  3. If we use both ensemble in production phase system might be NVPT
  like during production phase.

You cannot have an NVPT ensemble, i.e one with constant volume that is
coupled to a pressure bath.

  4. If we run only without NPT ensemble during production phase its
  affect MD simulation ?

Yes. Only you can assess the impact on your objectives.

Mark


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End of gmx-users Digest, Vol 93, Issue 52
*




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Haresh Ajani
09925522578




--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] homodimer simulation




Kavyashree M wrote:

Dear user,

I simulated a homodimer of 238aa each with oplsaa forcefield
using gromacs-4.5.3. But while calculating the rmsf plot I got a
plot in which starting and ending residue were connected by a
straight line along with the actual rmsf plot. Also the two rmsf


That's probably some artifact of the plotting software and is not actually 
relevant.


plots that it gave were slightly different from each other in few
regions. I was expecting similar rmsf for both the monomers.


If they are slightly different, that does not necessarily mean they are 
significantly different, and what you are observing is likely nothing more 
than the stochastic nature of MD.  Did you run only one simulation, or multiple? 
 How did you assess convergence?  It is highly unlikely to me that any MD 
simulation will produce identical results, but rather will be within some 
definable value of standard deviation, standard error, etc.



I checked the pdb file generated after md run, it did not have chain
ID but two chains were present.

Kindly let me know what is wrong with rmsf? Or what is wrong with
simulation.



Likely nothing.

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Coupling groups - Thermostat

Dear Gmx Users,

My system includes: ions, water, two tubes made of carbon atoms, protein.
I would like to run NVT (and then NPT) with position restarined dynamics of
my protein and tubes.
I am wondering whether this approach is good (two coupling groups:
Protein_Tubes and Water_and_ions??

My thermostat in mdp file:

 Temperature coupling is on

tcoupl = V-rescale ;

tc_grps = Protein_Tubes Water_and_ions ; two coupling groups

tau_t = 0.1 0.1 ; time constant

ref_t = 298 298 ; reference temperature

Please, let me know whether this apporach is ok. How can I set tc_grps when
I want to add ligand?

Steven
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Re: [gmx-users] maxh not causing termination

2012-01-10 Thread Ben Reynwar

On Mon, Jan 9, 2012 at 3:46 PM, Mark Abraham mark.abra...@anu.edu.au wrote:
 On 10/01/2012 7:19 AM, Ben Reynwar wrote:

 On Tue, Dec 20, 2011 at 7:16 PM, Mark Abraham mark.abra...@anu.edu.au
 wrote:

 On 12/19/2011 1:51 PM, Ben Reynwar wrote:

 I'm having a problem with gromacs not terminating as expected when
 using the maxh option.
 It is an REMD simulation with 32 replicas.
 I'm specifying -maxh 24 and as expected see the following in the stderr
 output.

 Step 773882: Run time exceeded 23.760 hours, will terminate the run

 Step 773876: Run time exceeded 23.760 hours, will terminate the run

 Step 773880: Run time exceeded 23.760 hours, will terminate the run

 etc

 However I can see that the output files continued to be written for
 another hour until at 25 hours the simulation was terminated by the
 queueing system.
 No checkpoint files were produced.  The output files show that the
 simulation continued until about step 797000.

 I've done similar things previously without running into this problem.
  Anyone have any ideas for what stupid mistake I could be making?

 Perhaps none. What GROMACS version is this? Does the latest version have the
 same behaviour?

 Mark

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 Sorry for the slow response.  I've been away on holiday.

 The version used is 4.5.5 with a bug fix applied from
 http://lists.gromacs.org/pipermail/gmx-developers/2011-October/005405.html
 It was a replica exchange simulation.

 I've narrowed down the problem to be specific to using infinite
 cutoff.  With a finite cutoff there are no problems.

 The initial run works fine and creates checkpoints.  However a run
 started from one of these checkpoints fails to create checkpoints
 itself.


 All that sounds very much like a bug. Please open an issue here
 http://redmine.gromacs.org and attach the lowest four .tpr and .cpt input
 files for the failing case. This will allow someone to find out why and
 perhaps fix it.

 Mark

Done (http://redmine.gromacs.org/issues/860)



 The diff between the an mdp that works fine and one that doesn't is:

 53,57c53,58
  ; [nm] cut-off distance for the short-range neighbor list.
  ; Set to zero for infinite cut-off.
  rlist = 0
  ; Recalculating pair-list is not necessary with an infinite cut-off
  nstlist = 0
 ---

 ; [nm] cut-off distance for the short-range neighbor list
 ; For Generalized Born this must be equal to the cut-off length for
 ; the born radius calculation.
 rlist = 1.6
 ; [steps] freq to update neighbor list
 nstlist = 1

 67,68c68,69
  ; infinite coloumb cut-off radius
  rcoulomb = 0
 ---

 ; coloumb cutoff radius
 rcoulomb = 1.6

 76,77c77,78
  ; Infinite VsW cutoff radius.
  rvdw = 0
 ---

 ; Increasing VdW cutoff to same as everything else.
 rvdw = 1.6

 144c145
  rgbradii = 0
 ---

 rgbradii = 1.6

 The complete offending mdp file will follow.
 Also if there's anything stupid in here unrelated to my current
 problem, please let me know too :).

 ; 7.3.2 Preprocssing
 ; --
 ; Apply constaint to alpha carbon atoms in alpha-crystalline domain.
 define = -DALPHACRYST_POSRES -DCHIRRES

 ; 7.3.3 Run Control
 ; -
 ; group(s) for center of mass motion removal
 comm_grps = System
 ; Do Langevin dynamics.
 integrator = sd
 ; maximum number of steps to integrate
 nsteps = 1
 ; remove center of mass translation and rotation around centre of mass
 comm_mode = Angular
 ; [ps] time step for integration
 dt = 0.002
 ; [steps] frequency of mass motion removal
 nstcomm = 10
 ; [ps] starting time for run
 tinit = 0

 ; 7.3.4 Langevin Dynamics
 ; ---
 ; Use PID to seed random number.
 ld_seed = -1

 ; 7.3.8 Output Control
 ; 
 ; [steps] freq to write velocities to trajectory
 nstvout = 0
 ; [steps] freq to write energies to log file
 nstlog = 1000
 ; [steps] freq to write energies to energy file
 nstenergy = 1000
 ; group(s) to write to xtc trajectory
 xtc_grps = System
 ; [real] precision to write xtc trajectory
 xtc_precision = 1000
 ; [steps] freq to write coordinates to xtc trajectory
 nstxtcout = 1000
 ; [steps] freq to write coordinates to trajectory
 nstxout = 0
 ; group(s) to write to energy file
 energygrps = System
 ; [steps] freq to write forces to trajectory
 nstfout = 0

 ; 7.3.9 Neighbour Searching
 ; -
 ; [nm] cut-off distance for the short-range neighbor list.
 ; Set to zero for infinite cut-off.
 rlist = 0
 ; Recalculating pair-list is not necessary with an infinite cut-off

[gmx-users] Concatenating RMSD plots

2012-01-10 Thread Rohit Farmer


Hi there,

I have just run several simulations of my system using different seeds 
and now i want to plot the RMSDs for different seeds in one plot for 
comparison. Is there any way to do it.


Thanks

Rohit

--
Rohit Farmer
PhD Biosciences (2011-2014)
Center for Systems Biology
University of Birmingham
Birmingham B152TT
United Kingdom
Email : rohit.far...@gmail.com

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Re: Fw: [gmx-users] trjconv in martini

2012-01-10 Thread mohammad agha

Hi Tsjerk,

I know that my question is silly but please help me.

I installed python2.5 on my system, then I ran ./xtcrev.py 1a.xtc  
1a-rev.xtc but it gave me following error:

Traceback (most recent call last):
  File ./xtcrev.py, line 54, in module
    n   = 92 + i(f.read(84)[-4:])   # Size of frame in bytes
  File ./xtcrev.py, line 24, in i
    def i(x): return sum([ord(x[j])(24-j*8) for j in range(4)])
IndexError: string index out of range

I know that j is out of range but I don't know that what should I do exactly?

May I ask you to help me, Please?

Best Regards
Sara



 From: Tsjerk Wassenaar tsje...@gmail.com
To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users 
gmx-users@gromacs.org 
Sent: Saturday, December 31, 2011 3:41 PM
Subject: Re: Fw: [gmx-users] trjconv in martini
 
Hi Sara,

 # Extract the first part of the trajectory
 trjconv -s md.tpr -f md.trr -n index.ndx -o 1a.xtc -e 1

That should be -e 19 :) But you can also use -e 20. Probably
that is better. I first thought it'd be better to avoid a double
frame, but since trjcat is used to combine the parts again, it doesn't
matter.

Good luck,

Tsjerk



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
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Re: [gmx-users] Coupling groups - Thermostat




Steven Neumann wrote:

Dear Gmx Users,
 
My system includes: ions, water, two tubes made of carbon atoms, protein.
I would like to run NVT (and then NPT) with position restarined dynamics 
of my protein and tubes.
I am wondering whether this approach is good (two coupling groups: 
Protein_Tubes and Water_and_ions??
 
My thermostat in mdp file:
 
 Temperature coupling is on


tcoupl = V-rescale ;

tc_grps = Protein_Tubes Water_and_ions ; two coupling groups

tau_t = 0.1 0.1 ; time constant

ref_t = 298 298 ; reference temperature

Please, let me know whether this apporach is ok. How can I set tc_grps 
when I want to add ligand?




I don't know a definitive answer here, so I'll throw out some ideas and 
hopefully stimulate some discussion.  I create tc_grps based on species whose 
dynamics are intimately linked.  For solvent, that includes water and ions.  Are 
your protein and tube physically associated?  If not, it doesn't make sense to 
me to couple them together.  In reality, no group should ever be coupled 
independently, but limitations in thermostats make it necessary.


Regarding the ligand, where is it?  Floating around in solvent, bound to the 
protein, or in the tube?  The answer to that question motivates how you treat it.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Concatenating RMSD plots




Rohit Farmer wrote:

Hi there,

I have just run several simulations of my system using different seeds 
and now i want to plot the RMSDs for different seeds in one plot for 
comparison. Is there any way to do it.




Import multiple data sets into xmgrace.  Alternatively, if they're all named 
something convenient (i.e. rmsd1.xvg, rmsd2.xvg, etc) load them from the command 
line:


xmgrace rmsd*.xvg 

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Coupling groups - Thermostat

On Tue, Jan 10, 2012 at 6:22 PM, Justin A. Lemkul jalem...@vt.edu wrote:

Steven Neumann wrote:

Dear Gmx Users,
My system includes: ions, water, two tubes made of carbon atoms, protein.
I would like to run NVT (and then NPT) with position restarined dynamics
of my protein and tubes.
I am wondering whether this approach is good (two coupling groups:
Protein_Tubes and Water_and_ions??
My thermostat in mdp file:
Temperature coupling is on

tcoupl = V-rescale ;

tc_grps = Protein_Tubes Water_and_ions ; two coupling groups

tau_t = 0.1 0.1 ; time constant

ref_t = 298 298 ; reference temperature

Please, let me know whether this apporach is ok. How can I set tc_grps
when I want to add ligand?

I don't know a definitive answer here, so I'll throw out some ideas and
hopefully stimulate some discussion. I create tc_grps based on species
whose dynamics are intimately linked. For solvent, that includes water and
ions. Are your protein and tube physically associated?

They are not physically associated but I put my protein as close as
possible to the tube and I want to run position restrained dynamics of my
tube and first 4 residues of my protein (stimulating attached protein to my
tube).

If not, it doesn't make sense to me to couple them together. In reality,
no group should ever be coupled independently, but limitations in
thermostats make it necessary.

Would you suggest specifing 3 groups in this case: Protein, Tube,
Water_and_ions ?

Regarding the ligand, where is it? Floating around in solvent, bound to
the protein, or in the tube? The answer to that question motivates how you
treat it.

With this simulation there is no ligand. My next simulation will be with
10-20 ligands placed randomly around the protein. I want to assess the
influence of lmy ligands to the stability of the protein, that is why I
need a comparison (in water only and in water with ligands).
I am wondering how to specify coupling groups in this case.

Steven

-Justin

--
==**==

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

==**==
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Re: [gmx-users] Coupling groups - Thermostat

On Tue, Jan 10, 2012 at 6:55 PM, Steven Neumann s.neuman...@gmail.comwrote:

On Tue, Jan 10, 2012 at 6:22 PM, Justin A. Lemkul jalem...@vt.edu wrote:

Steven Neumann wrote:

Dear Gmx Users,
My system includes: ions, water, two tubes made of carbon atoms,
protein.
I would like to run NVT (and then NPT) with position restarined dynamics
of my protein and tubes.
I am wondering whether this approach is good (two coupling groups:
Protein_Tubes and Water_and_ions??
My thermostat in mdp file:
Temperature coupling is on

tcoupl = V-rescale ;

tc_grps = Protein_Tubes Water_and_ions ; two coupling groups

tau_t = 0.1 0.1 ; time constant

ref_t = 298 298 ; reference temperature

Please, let me know whether this apporach is ok. How can I set tc_grps
when I want to add ligand?

Will you suggest attaching my protein directly to my tube in this case?

If not, it doesn't make sense to me to couple them together. In reality,
no group should ever be coupled independently, but limitations in
thermostats make it necessary.

Would you suggest specifing 3 groups in this case: Protein, Tube,
Water_and_ions ?

Regarding the ligand, where is it? Floating around in solvent, bound to
the protein, or in the tube? The answer to that question motivates how you
treat it.

Steven

-Justin

--
==**==

[gmx-users] Re: gmx-users Digest, Vol 93, Issue 54

2012-01-10 Thread Rohit Farmer


On 10/01/12 18:56, gmx-users-requ...@gromacs.org wrote:

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When replying, please edit your Subject line so it is more specific
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Today's Topics:

1. Concatenating RMSD plots (Rohit Farmer)
2. Re: Fw: [gmx-users] trjconv in martini (mohammad agha)
3. Re: Coupling groups - Thermostat (Justin A. Lemkul)
4. Re: Concatenating RMSD plots (Justin A. Lemkul)
5. Re: Coupling groups - Thermostat (Steven Neumann)


--

Message: 1
Date: Tue, 10 Jan 2012 17:23:07 +
From: Rohit Farmerrohit.bioi...@gmail.com
Subject: [gmx-users] Concatenating RMSD plots
To: gmx-users@gromacs.org
Message-ID:4f0c73fb.5010...@gmail.com
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi there,

I have just run several simulations of my system using different seeds
and now i want to plot the RMSDs for different seeds in one plot for
comparison. Is there any way to do it.

Thanks

Rohit


Hi Justin,

Thanks for the suggestion, I tried it and it works. Just one silly 
question do you have any idea how to control the color coding for 
different graphs like how can i know that the red one is the first and 
black is the second. Is there any option which I can specify etc.


Thanks

Rohit

--
Rohit Farmer
PhD Biosciences (2011-2014)
Center for Systems Biology
University of Birmingham
Birmingham B152TT
United Kingdom
Email : rohit.far...@gmail.com

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Re: [gmx-users] Concatenating RMSD plots




Rohit Farmer wrote:


Hi there,

I have just run several simulations of my system using different seeds
and now i want to plot the RMSDs for different seeds in one plot for
comparison. Is there any way to do it.

Thanks

Rohit


Hi Justin,

Thanks for the suggestion, I tried it and it works. Just one silly 
question do you have any idea how to control the color coding for 
different graphs like how can i know that the red one is the first and 
black is the second. Is there any option which I can specify etc.




Double-click the plotting area and you can change all sorts of attributes. 
Refer to the xmgrace documentation and tutorial material for more on such topics.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Coupling groups - Thermostat




Steven Neumann wrote:



On Tue, Jan 10, 2012 at 6:55 PM, Steven Neumann s.neuman...@gmail.com 
mailto:s.neuman...@gmail.com wrote:




On Tue, Jan 10, 2012 at 6:22 PM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:



Steven Neumann wrote:

Dear Gmx Users,
 My system includes: ions, water, two tubes made of carbon
atoms, protein.
I would like to run NVT (and then NPT) with position
restarined dynamics of my protein and tubes.
I am wondering whether this approach is good (two coupling
groups: Protein_Tubes and Water_and_ions??
 My thermostat in mdp file:
 Temperature coupling is on

tcoupl = V-rescale ;

tc_grps = Protein_Tubes Water_and_ions ; two coupling groups

tau_t = 0.1 0.1 ; time constant

ref_t = 298 298 ; reference temperature

Please, let me know whether this apporach is ok. How can I
set tc_grps when I want to add ligand?


I don't know a definitive answer here, so I'll throw out some
ideas and hopefully stimulate some discussion.  I create tc_grps
based on species whose dynamics are intimately linked.  For
solvent, that includes water and ions.  Are your protein and
tube physically associated? 



They are not physically associated but I put my protein as close as
possible to the tube and I want to run position restrained dynamics
of my tube and first 4 residues of my protein (stimulating attached
protein to my tube).


Will you suggest attaching my protein directly to my tube in this case?




I'm assuming by attaching you mean coupling in the same tc_grp?  I wouldn't. 
This is a complex case (and again, I don't know a true answer here) - your 
system has the potential to be highly dynamic.  Say the protein and tube bind, 
in which case they would (in theory) be coupled together.  Say they never bind, 
and then if you couple them together they shouldn't be.  You don't know a priori 
which way it will go.


 


 If not, it doesn't make sense to me to couple them together. In
reality, no group should ever be coupled independently, but
limitations in thermostats make it necessary.


Would you suggest specifing 3 groups in this case: Protein, Tube,
Water_and_ions ?



Sounds about as good as any approach.  It's where I'd start.



Regarding the ligand, where is it?  Floating around in solvent,
bound to the protein, or in the tube?  The answer to that
question motivates how you treat it.

With this simulation there is no ligand. My next simulation will be
with 10-20 ligands placed randomly around the protein. I want to
assess the influence of lmy ligands to the stability of the protein,
that is why I need a comparison (in water only and in water with
ligands).
I am wondering how to specify coupling groups in this case.



I would consider the ligands part of the solvent, because at such a high 
concentration, really what you're dealing with is almost a cosolvent situation. 
 Another example of species that may mix differently, aggregate, deposit on 
different surfaces, etc.  If there is existing literature on this topic (or even 
something peripherally related), try established protocols.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Coupling groups - Thermostat

On Tue, Jan 10, 2012 at 7:07 PM, Justin A. Lemkul jalem...@vt.edu wrote:

Steven Neumann wrote:

On Tue, Jan 10, 2012 at 6:55 PM, Steven Neumann
s.neuman...@gmail.commailto:
s.neuman...@gmail.com** wrote:

On Tue, Jan 10, 2012 at 6:22 PM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:

Steven Neumann wrote:

Dear Gmx Users,
My system includes: ions, water, two tubes made of carbon
atoms, protein.
I would like to run NVT (and then NPT) with position
restarined dynamics of my protein and tubes.
I am wondering whether this approach is good (two coupling
groups: Protein_Tubes and Water_and_ions??
My thermostat in mdp file:
Temperature coupling is on

tcoupl = V-rescale ;

tc_grps = Protein_Tubes Water_and_ions ; two coupling groups

tau_t = 0.1 0.1 ; time constant

ref_t = 298 298 ; reference temperature

Please, let me know whether this apporach is ok. How can I
set tc_grps when I want to add ligand?

I don't know a definitive answer here, so I'll throw out some
ideas and hopefully stimulate some discussion. I create tc_grps
based on species whose dynamics are intimately linked. For
solvent, that includes water and ions. Are your protein and
tube physically associated?

They are not physically associated but I put my protein as close as
possible to the tube and I want to run position restrained dynamics
of my tube and first 4 residues of my protein (stimulating attached
protein to my tube).

Will you suggest attaching my protein directly to my tube in this case?

I'm assuming by attaching you mean coupling in the same tc_grp? I
wouldn't. This is a complex case (and again, I don't know a true answer
here) - your system has the potential to be highly dynamic. Say the
protein and tube bind, in which case they would (in theory) be coupled
together. Say they never bind, and then if you couple them together they
shouldn't be. You don't know a priori which way it will go.

No. I mean physically attached. That is why my first 4 resiudes are closed
to the tube and position restrained. The best would be to attach it
physically by sharing one atom. No clue how. My tube is a representation of
the rest of the protein assembly (I am interested in the influence of
charged residues represented by ions and non charged by carbon atoms
within my tube - position restrained dynamics the tube) on my protein. What
is more there is another tube above my protein (not attached) and I am
interested also on the influence of those residues of the tube on my
protein conformation. In future I want to do Umrella Sampling pulling my
tube above to see free energy difference.

If not, it doesn't make sense to me to couple them together. In
reality, no group should ever be coupled independently, but
limitations in thermostats make it necessary.

Would you suggest specifing 3 groups in this case: Protein, Tube,
Water_and_ions ?

Sounds about as good as any approach. It's where I'd start.

Regarding the ligand, where is it? Floating around in solvent,
bound to the protein, or in the tube? The answer to that
question motivates how you treat it.

With this simulation there is no ligand. My next simulation will be
with 10-20 ligands placed randomly around the protein. I want to
assess the influence of lmy ligands to the stability of the protein,
that is why I need a comparison (in water only and in water with
ligands).
I am wondering how to specify coupling groups in this case.

I would consider the ligands part of the solvent, because at such a high
concentration, really what you're dealing with is almost a cosolvent
situation. Another example of species that may mix differently, aggregate,
deposit on different surfaces, etc. If there is existing literature on
this topic (or even something peripherally related), try established
protocols.

When I will add my ligands they will surely stack to the protein (maybe
tube as well...) . No clue what will happen between my protein and the tube
above.

Thank you,

Steven

-Justin

--
==**==

Re: [gmx-users] Coupling groups - Thermostat




Steven Neumann wrote:



On Tue, Jan 10, 2012 at 7:07 PM, Justin A. Lemkul jalem...@vt.edu 
mailto:jalem...@vt.edu wrote:




Steven Neumann wrote:



On Tue, Jan 10, 2012 at 6:55 PM, Steven Neumann
s.neuman...@gmail.com mailto:s.neuman...@gmail.com
mailto:s.neuman...@gmail.com mailto:s.neuman...@gmail.com__
wrote:



   On Tue, Jan 10, 2012 at 6:22 PM, Justin A. Lemkul
jalem...@vt.edu mailto:jalem...@vt.edu
   mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote:



   Steven Neumann wrote:

   Dear Gmx Users,
My system includes: ions, water, two tubes made of
carbon
   atoms, protein.
   I would like to run NVT (and then NPT) with position
   restarined dynamics of my protein and tubes.
   I am wondering whether this approach is good (two
coupling
   groups: Protein_Tubes and Water_and_ions??
My thermostat in mdp file:
Temperature coupling is on

   tcoupl = V-rescale ;

   tc_grps = Protein_Tubes Water_and_ions ; two coupling
groups

   tau_t = 0.1 0.1 ; time constant

   ref_t = 298 298 ; reference temperature

   Please, let me know whether this apporach is ok. How
can I
   set tc_grps when I want to add ligand?


   I don't know a definitive answer here, so I'll throw out some
   ideas and hopefully stimulate some discussion.  I create
tc_grps
   based on species whose dynamics are intimately linked.  For
   solvent, that includes water and ions.  Are your protein and
   tube physically associated?

   They are not physically associated but I put my protein as
close as
   possible to the tube and I want to run position restrained
dynamics
   of my tube and first 4 residues of my protein (stimulating
attached
   protein to my tube).


Will you suggest attaching my protein directly to my tube in
this case?



I'm assuming by attaching you mean coupling in the same tc_grp?  I
wouldn't. This is a complex case (and again, I don't know a true
answer here) - your system has the potential to be highly dynamic.
 Say the protein and tube bind, in which case they would (in theory)
be coupled together.  Say they never bind, and then if you couple
them together they shouldn't be.  You don't know a priori which way
it will go.


No. I mean physically attached. That is why my first 4 resiudes are 
closed to the tube and position restrained. The best would be to attach 
it physically by sharing one atom. No clue how. My tube is a 
representation of the rest of the protein assembly (I am interested in 
the influence of charged residues represented by ions and non charged 
by carbon atoms within my tube - position restrained dynamics the tube) 
on my protein. What is more there is another tube above my protein (not 
attached) and I am interested also on the influence of those residues 
of the tube on my protein conformation. In future I want to do Umrella 
Sampling pulling my tube above to see free energy difference.


 


It would have been better to state all of this up front ;)

If you are trying to create a single entity representing the protein and the 
tube, then yes, they should be a single tc_grp, and the best approach is to 
create a merged [moleculetype] definition with an actual bond between the shared 
atoms.  Doing so is not trivial, and I have no real quick way to suggest doing 
that, other than recreating a topology from pdb2gmx and perhaps making use of 
specbond.dat.  I'm still not 100% clear on where everything is located.


The other tube (not attached) and solvent/ions/ligands should likely be treated 
as separate groups for the purposes of temperature coupling.  But again, as 
stated, this is a very complicated system and the best methodology for 
simulating it is likely not defined terribly well.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Cytochrom C

2012-01-10 Thread Dariush Mohammadyani

Does anybody know where can I find [ HIS ] parameters?

Thanks,
Dariush


On Sat, Jan 7, 2012 at 3:58 AM, Dariush Mohammadyani 
d.mohammady...@gmail.com wrote:

 Dear Peter and Krzyszto,

 Thank you. I am following your comments. If I get any problem I will come
 back.




 On Fri, Jan 6, 2012 at 2:18 PM, Peter C. Lai p...@uab.edu wrote:

 He must be using an older version of Gromacs. 4.5.4 and lower don't have
 ACE in charmm27.

 On 2012-01-06 12:59:56PM -0600, Krzysztof Kuczera wrote:
  Here is the blocking group from
  gromacs-4.5.5/share/top/charmm27.ff/aminoacids.rtp
  KK
 
  [ ACE ]
[ atoms ]
   CH3 CT3 -0.270  0
   HH31HA  0.090   1
   HH32HA  0.090   2
   HH33HA  0.090   3
   C   C   0.510   4
   O   O   -0.510  5
[ bonds ]
   C   CH3
   C   +N
   CH3 HH31
   CH3 HH32
   CH3 HH33
   O   C
[ impropers ]
   C   CH3 +N  O
 
 
  On 1/6/12 12:40 PM, Peter C. Lai wrote:
   Corrected bonds section (sorry been up all night)
  
 [ ACE ]
  [ atoms ]
CH3CT3-0.270
HH31 HA  0.091
HH32 HA  0.092
HH33 HA  0.093
CC   0.514
OO  -0.515
  [ bonds ]
CH3HH31
CH3HH32
CH3HH33
CH3C
C  O
  
 Surprisingly, an .hdb entry for ACE exists so you don't need to
 create one.
   (and the .hdb entry uses HH3 as the base hydrogen name in ACE)
  
  
   On 2012-01-06 12:23:49PM -0600, Peter C. Lai wrote:
   Gromos96 53A6 has it.
  
   On 2012-01-06 01:18:38PM -0500, Dariush Mohammadyani wrote:
   I tried charmm27 too.
  
   Error:
   Residue 'ACE' not found in residue topology database
  
   I tried all forcefield in the list provided by pdb2gmx, but non
 of them
   works.
  
   Dariush
  
  
   On Thu, Jan 5, 2012 at 1:42 PM, Robert Hamersrjham...@wisc.edu
  wrote:
  
   HEME is in the charmm27 force field.
   bob h.
  
  
  
  
   On 1/5/2012 12:00 PM, Dariush Mohammadyani wrote:
  
   Yes, I have PDB file (1HRC.pdb). However, when I try to use
 pdb2gmx I
   get this error:
  
   Residue 'HEM' not found in residue topology database
  
   and HEM is Iron ion inside this protein. I do not know which
 forcefield is
   proper to use. I also tried MARTINI force field according their
 website; I
   used martinize.py script; Again I got error.
  
   Regards,
   Dariush
  
  
  
  
   On Thu, Jan 5, 2012 at 11:51 AM, Justin A. Lemkuljalem...@vt.edu
  wrote:
  
  
   Dariush Mohammadyani wrote:
  
   Hi all,
  
   Has anybody made initial configuration for Cytochrom C? Can it
 be shared
   with me?
  
  
 There are several in the PDB.
  
   -Justin
  
   --
   
  
   Justin A. Lemkul
   Ph.D. Candidate
   ICTAS Doctoral Scholar
   MILES-IGERT Trainee
   Department of Biochemistry
   Virginia Tech
   Blacksburg, VA
   jalemkul[at]vt.edu | (540) 231-9080
   http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
  
   
  
   --
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   http://lists.gromacs.org/mailman/listinfo/gmx-users
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 posting!
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   --
   Robert J. Hamers
   Wisconsin Distinguished Professor
   Univ. of Wisconsin-Madison
   1101 University Avenue
   Madison, WI 53706
   Ph: 608-262-6371
 Web: http://hamers.chem.wisc.edu
  
  
  
   --
   Kind Regards,
   Dariush Mohammadyani
   Department of Structural Biology
   University of Pittsburgh School of Medicine
   Biomedical Science Tower 3
   3501 Fifth Avenue
   Pittsburgh, PA 15261
   USA
   --
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   --
   ==
   Peter C. Lai  | University of Alabama-Birmingham
   Programmer/Analyst| KAUL 752A
   Genetics, Div. of Research| 705 South 20th Street
   p...@uab.edu   | Birmingham AL 35294-4461
   (205) 690-0808  |
   ==
  
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Re: [gmx-users] Cytochrom C




Dariush Mohammadyani wrote:

Does anybody know where can I find [ HIS ] parameters?



HIS is histidine; it's built into every one of the force fields in Gromacs.

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Cytochrom C

2012-01-10 Thread Dariush Mohammadyani

Dear Justin,
I could not find HIS in CHARMM and GROMOS53a6. Somebodies offer to rename
it to HSE or HSD, but I do not know why? and which one is correct. I am
working on Cytochorom c.

Thanks,
Dariush


On Tue, Jan 10, 2012 at 4:22 PM, Justin A. Lemkul jalem...@vt.edu wrote:



 Dariush Mohammadyani wrote:

 Does anybody know where can I find [ HIS ] parameters?


 HIS is histidine; it's built into every one of the force fields in Gromacs.


 -Justin

 --
 ==**==

 Justin A. Lemkul
 Ph.D. Candidate
 ICTAS Doctoral Scholar
 MILES-IGERT Trainee
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 ==**==
 --
 gmx-users mailing listgmx-users@gromacs.org
 http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users
 Please search the archive at http://www.gromacs.org/**
 Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore
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-- 
Kind Regards,
Dariush Mohammadyani
Department of Structural Biology
University of Pittsburgh School of Medicine
Biomedical Science Tower 3
3501 Fifth Avenue
Pittsburgh, PA 15261
USA
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Re: [gmx-users] Cytochrom C




Dariush Mohammadyani wrote:

Dear Justin,
I could not find HIS in CHARMM and GROMOS53a6. Somebodies offer to 
rename it to HSE or HSD, but I do not know why? and which one is 
correct. I am working on Cytochorom c.




They refer to different protonation states, either epsilon or delta.  The name 
in the .pdb file will be HIS (per standard nomenclature), but pdb2gmx will 
choose the protonation state it thinks is appropriate based on hydrogen bonding 
networks.  You can manually set protonation state with the -his flag.  For 53A6, 
HISA is delta protonation and HISB is epsilon.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Cytochrom C

2012-01-10 Thread Krzysztof Kuczera


Hi Dariush
If you are using the CHARMM27 force field, then all topology and parameters
are in your share/top/charmm27.ff directory
The defined molecules are listed in aminoacids.rtp and force field 
parameters in
numerous other files.  CHARMM does not use 'HIS' for histidine, but has 
HSD, HSE and HSP for the isomers with hydrogen at ND1, NE2 and both.
You can either set these isomers by hand - by editing your PDB file or 
use the

'pdb2gmx -his' option for interactive definition.

The bonus of keeping 'HIS' names and interactive setup is that bonds to heme
iron will be generated based on the 'specbond.dat' entries, if HIS NE2 
nitrogens are close enough to the FE.


Krzysztof


On 1/10/12 2:40 PM, Dariush Mohammadyani wrote:

Does anybody know where can I find [ HIS ] parameters?

Thanks,
Dariush


On Sat, Jan 7, 2012 at 3:58 AM, Dariush Mohammadyani 
d.mohammady...@gmail.com mailto:d.mohammady...@gmail.com wrote:


Dear Peter and Krzyszto,
Thank you. I am following your comments. If I get any problem I
will come back.


On Fri, Jan 6, 2012 at 2:18 PM, Peter C. Lai p...@uab.edu
mailto:p...@uab.edu wrote:

He must be using an older version of Gromacs. 4.5.4 and lower
don't have
ACE in charmm27.

On 2012-01-06 12 tel:2012-01-06%2012:59:56PM -0600,
Krzysztof Kuczera wrote:
 Here is the blocking group from
 gromacs-4.5.5/share/top/charmm27.ff/aminoacids.rtp
 KK

 [ ACE ]
   [ atoms ]
  CH3 CT3 -0.270  0
  HH31HA  0.090   1
  HH32HA  0.090   2
  HH33HA  0.090   3
  C   C   0.510   4
  O   O   -0.510  5
   [ bonds ]
  C   CH3
  C   +N
  CH3 HH31
  CH3 HH32
  CH3 HH33
  O   C
   [ impropers ]
  C   CH3 +N  O


 On 1/6/12 12:40 PM, Peter C. Lai wrote:
  Corrected bonds section (sorry been up all night)
 
[ ACE ]
 [ atoms ]
   CH3CT3-0.270
   HH31 HA  0.091
   HH32 HA  0.092
   HH33 HA  0.093
   CC   0.514
   OO  -0.515
 [ bonds ]
   CH3HH31
   CH3HH32
   CH3HH33
   CH3C
   C  O
 
Surprisingly, an .hdb entry for ACE exists so you don't
need to create one.
  (and the .hdb entry uses HH3 as the base hydrogen name in ACE)
 
 
  On 2012-01-06 12 tel:2012-01-06%2012:23:49PM -0600,
Peter C. Lai wrote:
  Gromos96 53A6 has it.
 
  On 2012-01-06 01 tel:2012-01-06%2001:18:38PM -0500,
Dariush Mohammadyani wrote:
  I tried charmm27 too.
 
  Error:
  Residue 'ACE' not found in residue topology database
 
  I tried all forcefield in the list provided by
pdb2gmx, but non of them
  works.
 
  Dariush
 
 
  On Thu, Jan 5, 2012 at 1:42 PM, Robert
Hamersrjham...@wisc.edu mailto:rjham...@wisc.edu  wrote:
 
  HEME is in the charmm27 force field.
  bob h.
 
 
 
 
  On 1/5/2012 12:00 PM, Dariush Mohammadyani wrote:
 
  Yes, I have PDB file (1HRC.pdb). However, when I try
to use pdb2gmx I
  get this error:
 
  Residue 'HEM' not found in residue topology database
 
  and HEM is Iron ion inside this protein. I do not know
which forcefield is
  proper to use. I also tried MARTINI force field
according their website; I
  used martinize.py script; Again I got error.
 
  Regards,
  Dariush
 
 
 
 
  On Thu, Jan 5, 2012 at 11:51 AM, Justin A.
Lemkuljalem...@vt.edu mailto:jalem...@vt.edu  wrote:
 
 
  Dariush Mohammadyani wrote:
 
  Hi all,
 
  Has anybody made initial configuration for Cytochrom
C? Can it be shared
  with me?
 
 
There are several in the PDB.
 
  -Justin
 
  --
  
 
  Justin A. Lemkul
  Ph.D. Candidate
  ICTAS Doctoral Scholar
  MILES-IGERT Trainee
  Department of Biochemistry
  Virginia Tech
  Blacksburg, VA
  jalemkul[at]vt.edu http://vt.edu | (540) 231-9080
tel:%28540%29%20231-9080

Re: [gmx-users] Coupling groups - Thermostat


On 11/01/2012 6:52 AM, Justin A. Lemkul wrote:



Steven Neumann wrote:



On Tue, Jan 10, 2012 at 7:07 PM, Justin A. Lemkul jalem...@vt.edu 
mailto:jalem...@vt.edu wrote:




Steven Neumann wrote:



On Tue, Jan 10, 2012 at 6:55 PM, Steven Neumann
s.neuman...@gmail.com mailto:s.neuman...@gmail.com
mailto:s.neuman...@gmail.com mailto:s.neuman...@gmail.com__
wrote:



   On Tue, Jan 10, 2012 at 6:22 PM, Justin A. Lemkul
jalem...@vt.edu mailto:jalem...@vt.edu
mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote:



   Steven Neumann wrote:

   Dear Gmx Users,
My system includes: ions, water, two tubes made of
carbon
   atoms, protein.
   I would like to run NVT (and then NPT) with position
   restarined dynamics of my protein and tubes.
   I am wondering whether this approach is good (two
coupling
   groups: Protein_Tubes and Water_and_ions??
My thermostat in mdp file:
Temperature coupling is on

   tcoupl = V-rescale ;

   tc_grps = Protein_Tubes Water_and_ions ; two coupling
groups

   tau_t = 0.1 0.1 ; time constant

   ref_t = 298 298 ; reference temperature

   Please, let me know whether this apporach is ok. How
can I
   set tc_grps when I want to add ligand?


   I don't know a definitive answer here, so I'll throw 
out some

   ideas and hopefully stimulate some discussion.  I create
tc_grps
   based on species whose dynamics are intimately 
linked.  For
   solvent, that includes water and ions.  Are your 
protein and

   tube physically associated?

   They are not physically associated but I put my protein as
close as
   possible to the tube and I want to run position restrained
dynamics
   of my tube and first 4 residues of my protein (stimulating
attached
   protein to my tube).


Will you suggest attaching my protein directly to my tube in
this case?



I'm assuming by attaching you mean coupling in the same tc_grp?  I
wouldn't. This is a complex case (and again, I don't know a true
answer here) - your system has the potential to be highly dynamic.
 Say the protein and tube bind, in which case they would (in theory)
be coupled together.  Say they never bind, and then if you couple
them together they shouldn't be.  You don't know a priori which way
it will go.


No. I mean physically attached. That is why my first 4 resiudes are 
closed to the tube and position restrained. The best would be to 
attach it physically by sharing one atom. No clue how. My tube is a 
representation of the rest of the protein assembly (I am interested 
in the influence of charged residues represented by ions and non 
charged by carbon atoms within my tube - position restrained dynamics 
the tube) on my protein. What is more there is another tube above my 
protein (not attached) and I am interested also on the influence of 
those residues of the tube on my protein conformation. In future I 
want to do Umrella Sampling pulling my tube above to see free energy 
difference.





It would have been better to state all of this up front ;)

If you are trying to create a single entity representing the protein 
and the tube, then yes, they should be a single tc_grp, and the best 
approach is to create a merged [moleculetype] definition with an 
actual bond between the shared atoms.  Doing so is not trivial, and I 
have no real quick way to suggest doing that, other than recreating a 
topology from pdb2gmx and perhaps making use of specbond.dat.  I'm 
still not 100% clear on where everything is located.


The other tube (not attached) and solvent/ions/ligands should likely 
be treated as separate groups for the purposes of temperature 
coupling.  But again, as stated, this is a very complicated system and 
the best methodology for simulating it is likely not defined terribly 
well.


One alternative is to pay attention to the advice at the end of section 
3.4.8 of the manual and ref cited there - that separate T-coupling 
groups can be worse than the problems they purport to fix.


Mark
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[gmx-users] HEME topology

Hello,

Can any one send topology for Heme group..My work is stuckeup

here are the PDB parameters for HEME

---

HETATM 3851 FE   HEM   482   4.876  25.216  23.893  1.00  0.00
HETATM 3852  CHA HEM   482   5.264  25.759  20.480  1.00  0.00
HETATM 3853  CHB HEM   482   8.132  24.660  24.172  1.00  0.00
HETATM 3854  CHC HEM   482   4.480  24.399  27.195  1.00  0.00
HETATM 3855  CHD HEM   482   1.700  25.148  23.458  1.00  0.00
HETATM 3856  NA  HEM   482   6.466  25.218  22.555  1.00  0.00
HETATM 3857  C1A HEM   482   6.439  25.484  21.193  1.00  0.00
HETATM 3858  C2A HEM   482   7.778  25.464  20.681  1.00  0.00
HETATM 3859  C3A HEM   482   8.610  25.197  21.767  1.00  0.00
HETATM 3860  C4A HEM   482   7.741  25.081  22.906  1.00  0.00
HETATM 3861  CMA HEM   482  10.215  25.091  21.758  1.00  0.00
HETATM 3862  CAA HEM   482   8.230  25.628  19.242  1.00  0.00
HETATM 3863  CBA HEM   482   8.574  27.061  18.804  1.00  0.00
HETATM 3864  CGA HEM   482   9.117  27.044  17.359  1.00  0.00
HETATM 3865  O1A HEM   482   9.982  27.831  17.013  1.00  0.00
HETATM 3866  O2A HEM   482   8.739  26.229  16.541  1.00  0.00
HETATM 3867  NB  HEM   482   6.104  24.497  25.449  1.00  0.00
HETATM 3868  C1B HEM   482   7.444  24.359  25.345  1.00  0.00
HETATM 3869  C2B HEM   482   8.044  24.034  26.598  1.00  0.00
HETATM 3870  C3B HEM   482   6.961  23.930  27.496  1.00  0.00
HETATM 3871  C4B HEM   482   5.778  24.182  26.693  1.00  0.00
HETATM 3872  CMB HEM   482   9.563  23.973  26.877  1.00  0.00
HETATM 3873  CAB HEM   482   6.964  23.552  28.851  1.00  0.00
HETATM 3874  CBB HEM   482   8.069  23.513  29.865  1.00  0.00
HETATM 3875  NC  HEM   482   3.315  24.748  25.179  1.00  0.00
HETATM 3876  C1C HEM   482   3.331  24.678  26.492  1.00  0.00
HETATM 3877  C2C HEM   482   2.053  24.644  27.006  1.00  0.00
HETATM 3878  C3C HEM   482   1.187  24.668  25.881  1.00  0.00
HETATM 3879  C4C HEM   482   2.053  24.742  24.763  1.00  0.00
HETATM 3880  CMC HEM   482   1.716  24.541  28.529  1.00  0.00
HETATM 3881  CAC HEM   482  -0.191  24.700  25.725  1.00  0.00
HETATM 3882  CBC HEM   482  -1.163  24.945  26.680  1.00  0.00
HETATM 3883  ND  HEM   482   3.655  25.286  22.181  1.00  0.00
HETATM 3884  C1D HEM   482   2.373  25.199  22.282  1.00  0.00
HETATM 3885  C2D HEM   482   1.768  25.396  21.008  1.00  0.00
HETATM 3886  C3D HEM   482   2.780  25.600  20.124  1.00  0.00
HETATM 3887  C4D HEM   482   3.958  25.545  20.924  1.00  0.00
HETATM 3888  CMD HEM   482   0.252  25.372  20.693  1.00  0.00
HETATM 3889  CAD HEM   482   2.755  25.897  18.597  1.00  0.00
HETATM 3890  CBD HEM   482   2.710  27.455  18.272  1.00  0.00
HETATM 3891  CGD HEM   482   2.759  27.846  16.738  1.00  0.00
HETATM 3892  O1D HEM   482   2.411  29.018  16.323  1.00  0.00
HETATM 3893  O2D HEM   482   3.210  26.948  15.911  1.00  0.00
TER3894  HEM   482



thanks in advance

nirmal
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RE: [gmx-users] HEME topology

2012-01-10 Thread Anik Sen

Dear nirmal,
  try prodrg server for generating the topology file for 
the said pdb file. Here is the link. http://davapc1.bioch.dundee.ac.uk/prodrg/


From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Nirmal Prasad [nimmynir...@gmail.com]
Sent: Wednesday, January 11, 2012 9:45 AM
To: Discussion list for GROMACS users
Subject: [gmx-users] HEME topology

Hello,

Can any one send topology for Heme group..My work is stuckeup

here are the PDB parameters for HEME

---

HETATM 3851 FE   HEM   482   4.876  25.216  23.893  1.00  0.00
HETATM 3852  CHA HEM   482   5.264  25.759  20.480  1.00  0.00
HETATM 3853  CHB HEM   482   8.132  24.660  24.172  1.00  0.00
HETATM 3854  CHC HEM   482   4.480  24.399  27.195  1.00  0.00
HETATM 3855  CHD HEM   482   1.700  25.148  23.458  1.00  0.00
HETATM 3856  NA  HEM   482   6.466  25.218  22.555  1.00  0.00
HETATM 3857  C1A HEM   482   6.439  25.484  21.193  1.00  0.00
HETATM 3858  C2A HEM   482   7.778  25.464  20.681  1.00  0.00
HETATM 3859  C3A HEM   482   8.610  25.197  21.767  1.00  0.00
HETATM 3860  C4A HEM   482   7.741  25.081  22.906  1.00  0.00
HETATM 3861  CMA HEM   482  10.215  25.091  21.758  1.00  0.00
HETATM 3862  CAA HEM   482   8.230  25.628  19.242  1.00  0.00
HETATM 3863  CBA HEM   482   8.574  27.061  18.804  1.00  0.00
HETATM 3864  CGA HEM   482   9.117  27.044  17.359  1.00  0.00
HETATM 3865  O1A HEM   482   9.982  27.831  17.013  1.00  0.00
HETATM 3866  O2A HEM   482   8.739  26.229  16.541  1.00  0.00
HETATM 3867  NB  HEM   482   6.104  24.497  25.449  1.00  0.00
HETATM 3868  C1B HEM   482   7.444  24.359  25.345  1.00  0.00
HETATM 3869  C2B HEM   482   8.044  24.034  26.598  1.00  0.00
HETATM 3870  C3B HEM   482   6.961  23.930  27.496  1.00  0.00
HETATM 3871  C4B HEM   482   5.778  24.182  26.693  1.00  0.00
HETATM 3872  CMB HEM   482   9.563  23.973  26.877  1.00  0.00
HETATM 3873  CAB HEM   482   6.964  23.552  28.851  1.00  0.00
HETATM 3874  CBB HEM   482   8.069  23.513  29.865  1.00  0.00
HETATM 3875  NC  HEM   482   3.315  24.748  25.179  1.00  0.00
HETATM 3876  C1C HEM   482   3.331  24.678  26.492  1.00  0.00
HETATM 3877  C2C HEM   482   2.053  24.644  27.006  1.00  0.00
HETATM 3878  C3C HEM   482   1.187  24.668  25.881  1.00  0.00
HETATM 3879  C4C HEM   482   2.053  24.742  24.763  1.00  0.00
HETATM 3880  CMC HEM   482   1.716  24.541  28.529  1.00  0.00
HETATM 3881  CAC HEM   482  -0.191  24.700  25.725  1.00  0.00
HETATM 3882  CBC HEM   482  -1.163  24.945  26.680  1.00  0.00
HETATM 3883  ND  HEM   482   3.655  25.286  22.181  1.00  0.00
HETATM 3884  C1D HEM   482   2.373  25.199  22.282  1.00  0.00
HETATM 3885  C2D HEM   482   1.768  25.396  21.008  1.00  0.00
HETATM 3886  C3D HEM   482   2.780  25.600  20.124  1.00  0.00
HETATM 3887  C4D HEM   482   3.958  25.545  20.924  1.00  0.00
HETATM 3888  CMD HEM   482   0.252  25.372  20.693  1.00  0.00
HETATM 3889  CAD HEM   482   2.755  25.897  18.597  1.00  0.00
HETATM 3890  CBD HEM   482   2.710  27.455  18.272  1.00  0.00
HETATM 3891  CGD HEM   482   2.759  27.846  16.738  1.00  0.00
HETATM 3892  O1D HEM   482   2.411  29.018  16.323  1.00  0.00
HETATM 3893  O2D HEM   482   3.210  26.948  15.911  1.00  0.00
TER3894  HEM   482



thanks in advance

nirmal
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Re: [gmx-users] Coupling groups - Thermostat

2012-01-10 Thread Tsjerk Wassenaar

Hey,

In addition to the foregoing...
The separate coupling is to prevent draining energy from one part to the
other. It is pretty unlikely that either protein or tube will drain the
other one. Water is always a different story.
You can check the setup you choose afterwards, like after a short run, by
rerunning the sinulation with the split groups and checking the
temperature. E.g. if you run with protein and tube in one group, the should
both end up having the same temperature, within the noise. Do mind the
noise is related to the number of atoms in a group.

Hope it helps,

Tsjerk

On Jan 11, 2012 12:00 AM, Mark Abraham mark.abra...@anu.edu.au wrote:

On 11/01/2012 6:52 AM, Justin A. Lemkul wrote: Steven Neumann
wrote: On Tue, Jan...
One alternative is to pay attention to the advice at the end of section
3.4.8 of the manual and ref cited there - that separate T-coupling groups
can be worse than the problems they purport to fix.

Mark

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Re: [gmx-users] Coupling groups - Thermostat


On 11/01/2012 4:23 PM, Tsjerk Wassenaar wrote:


Hey,

In addition to the foregoing...
The separate coupling is to prevent draining energy from one part to 
the other. It is pretty unlikely that either protein or tube will 
drain the other one. Water is always a different story.
You can check the setup you choose afterwards, like after a short run, 
by rerunning the sinulation with the split groups and checking the 
temperature. E.g. if you run with protein and tube in one group, the 
should both end up having the same temperature, within the noise. Do 
mind the noise is related to the number of atoms in a group.




Clarifying - the amount of noise is *inversely* related to the number 
atoms. That should be fairly moot, though, because a T-coupling group 
with less than a thousand atoms is probably not worth considering. The 
algorithms work best in macroscopic limits, so a group that's not at 
least 10% of your system is likely not approaching that limit - and 
grompp will warn you about that.


Mark


Hope it helps,

Tsjerk

On Jan 11, 2012 12:00 AM, Mark Abraham mark.abra...@anu.edu.au 
mailto:mark.abra...@anu.edu.au wrote:


On 11/01/2012 6:52 AM, Justin A. Lemkul wrote: Steven Neumann 
wrote: On Tue, Jan...


One alternative is to pay attention to the advice at the end of 
section 3.4.8 of the manual and ref cited there - that separate 
T-coupling groups can be worse than the problems they purport to fix.


Mark

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mailto:gmx-users@gromacs.org 
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Fw: Fw: [gmx-users] trjconv in martini

2012-01-10 Thread mohammad agha




- Forwarded Message -
From: mohammad agha mra...@yahoo.com
To: gmx-users@gromacs.org gmx-users@gromacs.org 
Sent: Tuesday, January 10, 2012 9:08 PM
Subject: Re: Fw: [gmx-users] trjconv in martini
 

Hi Tsjerk,

I know that my question is silly but please help me.

I installed python2.5 on my system, then I ran ./xtcrev.py 1a.xtc  
1a-rev.xtc but it gave me following error:

Traceback (most recent call last):
  File ./xtcrev.py, line 54, in module
    n   = 92 + i(f.read(84)[-4:])   # Size of frame in bytes
  File ./xtcrev.py, line 24, in i
    def i(x): return sum([ord(x[j])(24-j*8) for j in range(4)])
IndexError: string index out of range

I know that j is out of range but I don't know that what should I do exactly?

May I ask you to help me, Please?

Best Regards
Sara


 From: Tsjerk Wassenaar tsje...@gmail.com
To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users 
gmx-users@gromacs.org 
Sent: Saturday, December 31, 2011 3:41 PM
Subject: Re: Fw: [gmx-users] trjconv in martini
 
Hi Sara,

 # Extract the first part of the trajectory
 trjconv -s md.tpr -f md.trr -n index.ndx -o 1a.xtc -e 1

That should be -e 19 :) But you can also use -e 20. Probably
that is better. I first thought it'd be better to avoid a double
frame, but since trjcat is used to combine the parts again, it doesn't
matter.

Good luck,

Tsjerk



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands



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Re: [gmx-users] Hello