RE: [gmx-users] make_ndx

2007-09-26 Thread Naser, Md Abu 
Thanks XAvier and David!
I think I know what I need to do to 
get my group.

With regards,

Abu Naser 

School Of Life Sciences 
Heriot-Watt University 
Edinburgh EH14 4AS 
Email: [EMAIL PROTECTED]
Phone: +44(0)1314518265 
Fax : +44(0) 131 451 3009 


 



-Original Message-
From: [EMAIL PROTECTED] on behalf of David van der Spoel
Sent: Thu 27/09/2007 7:29 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] make_ndx
 
Naser, Md Abu wrote:
> Thanks david!
> 
oops I misread. Sidechains do not contain C-alpha (which you can easily 
check in the index file).
So within make_ndx type h for help on joining the two.

> 
> 
> Abu Naser
> 
> School Of Life Sciences
> Heriot-Watt University
> Edinburgh EH14 4AS
> Email: [EMAIL PROTECTED]
> Phone: +44(0)1314518265
> Fax : +44(0) 131 451 3009
> 
> 
> 
> 
> 
> 
> -Original Message-
> From: [EMAIL PROTECTED] on behalf of David van der Spoel
> Sent: Thu 27/09/2007 7:17 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] make_ndx
> 
> Naser, Md Abu wrote:
>  > Hi XAvier,
>  >
>  > "Single out" I mean  pick up only the side chain bonded with alpha
>  > carbon atom and
>  > put them in a group using make_ndx.
>  >
> all side chains are.
> and sidechain is a default group.
> 
>  > With regards,
>  > 
>  >
>  > Abu Naser
>  >
>  > School Of Life Sciences
>  > Heriot-Watt University
>  > Edinburgh EH14 4AS
>  > Email: [EMAIL PROTECTED]
>  > Phone: +44(0)1314518265
>  > Fax : +44(0) 131 451 3009
>  >
>  >
>  >
>  >
>  >
>  >
>  > -Original Message-
>  > From: [EMAIL PROTECTED] on behalf of Xavier Periole
>  > Sent: Wed 26/09/2007 8:42 PM
>  > To: Discussion list for GROMACS users
>  > Subject: Re: [gmx-users] make_ndx
>  >
>  > On Wed, 26 Sep 2007 20:08:06 +0100
>  >   "Naser, Md Abu" <[EMAIL PROTECTED]> wrote:
>  >  > Hi All User,
>  >  >
>  >  > Is there anyway I can single out side chain of alpha carbon atom using
>  >  >make_ndx?
>  >
>  > What do you mean by "single out"
>  > and with "side chain of alpha carbon" ?
>  >
>  >  >
>  >  > Thanks in advance.
>  >  >
>  >  > Abu Naser
>  >  >
>  >  > School Of Life Sciences
>  >  > Heriot-Watt University
>  >  > Edinburgh EH14 4AS
>  >  > Email: [EMAIL PROTECTED]
>  >  > Phone: +44(0)1314518265
>  >  >Fax : +44(0) 131 451 3009
>  >  >
>  >  >
>  >  >
>  >  >
>  >
>  > -
>  > XAvier Periole - PhD
>  >
>  > 1- Institute of Molecular Assemblies
>  >   City University of New York - USA
>  > 2- Molecular Dynamics-Group
>  >   University of Groningen - The Netherlands
>  > http://md.chem.rug.nl/~periole
>  > -
>  > ___
>  > gmx-users mailing listgmx-users@gromacs.org
>  > http://www.gromacs.org/mailman/listinfo/gmx-users
>  > Please search the archive at http://www.gromacs.org/search before 
> posting!
>  > Please don't post (un)subscribe requests to the list. Use the
>  > www interface or send it to [EMAIL PROTECTED]
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>  >
>  >
>  > 
>  >
>  > ___
>  > gmx-users mailing listgmx-users@gromacs.org
>  > http://www.gromacs.org/mailman/listinfo/gmx-users
>  > Please search the archive at http://www.gromacs.org/search before 
> posting!
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>  > www interface or send it to [EMAIL PROTECTED]
>  > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 
> --
> David.
> 
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,  75124 Uppsala, Sweden
> phone:  46 18 471 4205  fax: 46 18 511 755
> [EMAIL PROTECTED][EMAIL PROTECTED]   http://folding.bmc.uu.se
> 
> ___
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> 
> 
> 
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Re: [gmx-users] make_ndx

2007-09-26 Thread David van der Spoel 

Naser, Md Abu wrote:

Thanks david!

oops I misread. Sidechains do not contain C-alpha (which you can easily 
check in the index file).

So within make_ndx type h for help on joining the two.




Abu Naser

School Of Life Sciences
Heriot-Watt University
Edinburgh EH14 4AS
Email: [EMAIL PROTECTED]
Phone: +44(0)1314518265
Fax : +44(0) 131 451 3009






-Original Message-
From: [EMAIL PROTECTED] on behalf of David van der Spoel
Sent: Thu 27/09/2007 7:17 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] make_ndx

Naser, Md Abu wrote:
 > Hi XAvier,
 >
 > "Single out" I mean  pick up only the side chain bonded with alpha
 > carbon atom and
 > put them in a group using make_ndx.
 >
all side chains are.
and sidechain is a default group.

 > With regards,
 > 
 >

 > Abu Naser
 >
 > School Of Life Sciences
 > Heriot-Watt University
 > Edinburgh EH14 4AS
 > Email: [EMAIL PROTECTED]
 > Phone: +44(0)1314518265
 > Fax : +44(0) 131 451 3009
 >
 >
 >
 >
 >
 >
 > -Original Message-
 > From: [EMAIL PROTECTED] on behalf of Xavier Periole
 > Sent: Wed 26/09/2007 8:42 PM
 > To: Discussion list for GROMACS users
 > Subject: Re: [gmx-users] make_ndx
 >
 > On Wed, 26 Sep 2007 20:08:06 +0100
 >   "Naser, Md Abu" <[EMAIL PROTECTED]> wrote:
 >  > Hi All User,
 >  >
 >  > Is there anyway I can single out side chain of alpha carbon atom using
 >  >make_ndx?
 >
 > What do you mean by "single out"
 > and with "side chain of alpha carbon" ?
 >
 >  >
 >  > Thanks in advance.
 >  >
 >  > Abu Naser
 >  >
 >  > School Of Life Sciences
 >  > Heriot-Watt University
 >  > Edinburgh EH14 4AS
 >  > Email: [EMAIL PROTECTED]
 >  > Phone: +44(0)1314518265
 >  >Fax : +44(0) 131 451 3009
 >  >
 >  >
 >  >
 >  >
 >
 > -
 > XAvier Periole - PhD
 >
 > 1- Institute of Molecular Assemblies
 >   City University of New York - USA
 > 2- Molecular Dynamics-Group
 >   University of Groningen - The Netherlands
 > http://md.chem.rug.nl/~periole
 > -
 > ___
 > gmx-users mailing listgmx-users@gromacs.org
 > http://www.gromacs.org/mailman/listinfo/gmx-users
 > Please search the archive at http://www.gromacs.org/search before 
posting!

 > Please don't post (un)subscribe requests to the list. Use the
 > www interface or send it to [EMAIL PROTECTED]
 > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
 >
 >
 > 
 >
 > ___
 > gmx-users mailing listgmx-users@gromacs.org
 > http://www.gromacs.org/mailman/listinfo/gmx-users
 > Please search the archive at http://www.gromacs.org/search before 
posting!

 > Please don't post (un)subscribe requests to the list. Use the
 > www interface or send it to [EMAIL PROTECTED]
 > Can't post? Read http://www.gromacs.org/mailing_lists/users.php


--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED][EMAIL PROTECTED]   http://folding.bmc.uu.se

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--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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Re: [gmx-users] make_ndx

2007-09-26 Thread Xavier Periole 

On Thu, 27 Sep 2007 07:08:00 +0100
 "Naser, Md Abu" <[EMAIL PROTECTED]> wrote:

Hi XAvier,

"Single out" I mean  pick up only the side chain bonded with alpha carbon 
atom and

put them in a group using make_ndx.


What about joining the groups "C-alpha" and "SideChain" using:
X | Y ; where X and Y are the numbers corresponding to the
groups.
Note that the C-beta is not included in the sidechain group.
you can add them by using something like:
a CB; which will create a new group.

This should be enough for you to get what you like.



With regards,
 

Abu Naser 

School Of Life Sciences 
Heriot-Watt University 
Edinburgh EH14 4AS 
Email: [EMAIL PROTECTED]
Phone: +44(0)1314518265 
Fax : +44(0) 131 451 3009 







-Original Message-
From: [EMAIL PROTECTED] on behalf of Xavier Periole
Sent: Wed 26/09/2007 8:42 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] make_ndx

On Wed, 26 Sep 2007 20:08:06 +0100
 "Naser, Md Abu" <[EMAIL PROTECTED]> wrote:

Hi All User,

Is there anyway I can single out side chain of alpha carbon atom using 
make_ndx?


What do you mean by "single out"
and with "side chain of alpha carbon" ?



Thanks in advance.

Abu Naser 

School Of Life Sciences 
Heriot-Watt University 
Edinburgh EH14 4AS 
Email: [EMAIL PROTECTED]
Phone: +44(0)1314518265 
Fax : +44(0) 131 451 3009 







-
XAvier Periole - PhD

1- Institute of Molecular Assemblies
 City University of New York - USA
2- Molecular Dynamics-Group
 University of Groningen - The Netherlands
http://md.chem.rug.nl/~periole
-
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-
XAvier Periole - PhD

1- Institute of Molecular Assemblies
 City University of New York - USA
2- Molecular Dynamics-Group
 University of Groningen - The Netherlands
http://md.chem.rug.nl/~periole
-
___
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RE: [gmx-users] make_ndx

2007-09-26 Thread Naser, Md Abu 
Thanks david! 



Abu Naser 

School Of Life Sciences 
Heriot-Watt University 
Edinburgh EH14 4AS 
Email: [EMAIL PROTECTED]
Phone: +44(0)1314518265 
Fax : +44(0) 131 451 3009 


 



-Original Message-
From: [EMAIL PROTECTED] on behalf of David van der Spoel
Sent: Thu 27/09/2007 7:17 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] make_ndx
 
Naser, Md Abu wrote:
> Hi XAvier,
> 
> "Single out" I mean  pick up only the side chain bonded with alpha 
> carbon atom and
> put them in a group using make_ndx.
> 
all side chains are.
and sidechain is a default group.

> With regards,
>  
> 
> Abu Naser
> 
> School Of Life Sciences
> Heriot-Watt University
> Edinburgh EH14 4AS
> Email: [EMAIL PROTECTED]
> Phone: +44(0)1314518265
> Fax : +44(0) 131 451 3009
> 
> 
> 
> 
> 
> 
> -Original Message-
> From: [EMAIL PROTECTED] on behalf of Xavier Periole
> Sent: Wed 26/09/2007 8:42 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] make_ndx
> 
> On Wed, 26 Sep 2007 20:08:06 +0100
>   "Naser, Md Abu" <[EMAIL PROTECTED]> wrote:
>  > Hi All User,
>  >
>  > Is there anyway I can single out side chain of alpha carbon atom using
>  >make_ndx?
> 
> What do you mean by "single out"
> and with "side chain of alpha carbon" ?
> 
>  >
>  > Thanks in advance.
>  >
>  > Abu Naser
>  >
>  > School Of Life Sciences
>  > Heriot-Watt University
>  > Edinburgh EH14 4AS
>  > Email: [EMAIL PROTECTED]
>  > Phone: +44(0)1314518265
>  >Fax : +44(0) 131 451 3009
>  >
>  >
>  >
>  >
> 
> -
> XAvier Periole - PhD
> 
> 1- Institute of Molecular Assemblies
>   City University of New York - USA
> 2- Molecular Dynamics-Group
>   University of Groningen - The Netherlands
> http://md.chem.rug.nl/~periole
> -
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to [EMAIL PROTECTED]
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 
> 
> 
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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> www interface or send it to [EMAIL PROTECTED]
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-- 
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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Re: [gmx-users] make_ndx

2007-09-26 Thread David van der Spoel 

Naser, Md Abu wrote:

Hi XAvier,

"Single out" I mean  pick up only the side chain bonded with alpha 
carbon atom and

put them in a group using make_ndx.


all side chains are.
and sidechain is a default group.


With regards,
 


Abu Naser

School Of Life Sciences
Heriot-Watt University
Edinburgh EH14 4AS
Email: [EMAIL PROTECTED]
Phone: +44(0)1314518265
Fax : +44(0) 131 451 3009






-Original Message-
From: [EMAIL PROTECTED] on behalf of Xavier Periole
Sent: Wed 26/09/2007 8:42 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] make_ndx

On Wed, 26 Sep 2007 20:08:06 +0100
  "Naser, Md Abu" <[EMAIL PROTECTED]> wrote:
 > Hi All User,
 >
 > Is there anyway I can single out side chain of alpha carbon atom using
 >make_ndx?

What do you mean by "single out"
and with "side chain of alpha carbon" ?

 >
 > Thanks in advance.
 >
 > Abu Naser
 >
 > School Of Life Sciences
 > Heriot-Watt University
 > Edinburgh EH14 4AS
 > Email: [EMAIL PROTECTED]
 > Phone: +44(0)1314518265
 >Fax : +44(0) 131 451 3009
 >
 >
 >
 >

-
XAvier Periole - PhD

1- Institute of Molecular Assemblies
  City University of New York - USA
2- Molecular Dynamics-Group
  University of Groningen - The Netherlands
http://md.chem.rug.nl/~periole
-
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--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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[gmx-users] fortran xtc reading problem?

2007-09-26 Thread Jones de Andrade 
Hi.

I'm trying to read some .xtc file trajectory files throw my fortran codes,
following the guidelines from
http://xray.bmc.uu.se/~spoel/md/online/xtc.html

Also later found this html file on the gromacs directory here.  ;)  Anyway,
I got stuck at some really strange point: I'm basically not finding the
library xtcf to link it to. In order to be completelly right, I'm not even
finding the "testxtcf.f" file that is supposed to be here.

There was anychange in file names and/or locations between those guidelines
and the actual distribution?

Thanks a lot in advance!

Sincerally yours,

Jones
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RE: [gmx-users] make_ndx

2007-09-26 Thread Naser, Md Abu 
Hi XAvier,

"Single out" I mean  pick up only the side chain bonded with alpha carbon atom 
and
put them in a group using make_ndx.

With regards,
  

Abu Naser 

School Of Life Sciences 
Heriot-Watt University 
Edinburgh EH14 4AS 
Email: [EMAIL PROTECTED]
Phone: +44(0)1314518265 
Fax : +44(0) 131 451 3009 


 



-Original Message-
From: [EMAIL PROTECTED] on behalf of Xavier Periole
Sent: Wed 26/09/2007 8:42 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] make_ndx
 
On Wed, 26 Sep 2007 20:08:06 +0100
  "Naser, Md Abu" <[EMAIL PROTECTED]> wrote:
> Hi All User,
> 
> Is there anyway I can single out side chain of alpha carbon atom using 
>make_ndx?

What do you mean by "single out"
and with "side chain of alpha carbon" ?

> 
> Thanks in advance.
> 
> Abu Naser 
> 
> School Of Life Sciences 
> Heriot-Watt University 
> Edinburgh EH14 4AS 
> Email: [EMAIL PROTECTED]
> Phone: +44(0)1314518265 
>Fax : +44(0) 131 451 3009 
> 
> 
> 
> 

-
XAvier Periole - PhD

1- Institute of Molecular Assemblies
  City University of New York - USA
2- Molecular Dynamics-Group
  University of Groningen - The Netherlands
http://md.chem.rug.nl/~periole
-
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Re: [gmx-users] the mkinl*.c and metacode.c sources

2007-09-26 Thread David van der Spoel 

renying wrote:
I am trying to build Gromacs using visual C++ with the workspace downloaded from ftp.gromacs.org. However the mkinl*.c and metacode.c sources, which are quested under '..\src\gmxlib\metacode.c', can not be found in Gromacs package. 
Whaere can I get them?


These files are not current any more. in 3.3 the files have been 
replaced by code in src/gmxlib/nonbonded/nb_kernel. With a proper 
(command line) make tool these will be built automatically.


We do not support MS tools for building gromacs and as said before I am 
not familiar with the concept of workspace.



--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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Re: [gmx-users] installation

2007-09-26 Thread David van der Spoel 

Mohammad Ahmadi wrote:

Hi all,

 

I am trying to install of  gromacs-3.3-1.i386.rpm in suse linux, but 
when I type:


rpm -ivh gromacs-3.3-1.i386.rpm

 


I get the follow error:

 

file /usr/bin/disco from install of gromacs-3.3-1 conflicts with file 
from package mono-web-1.1.13.8-2.7


file /usr/share/man/man1/disco.1.gz from install of gromacs-3.3-1 
conflicts with file from package mono-web-1.1.13.8-2.7


 


I would appreciate some suggestions in this relation.


the rpms are for redhat like systems. suse is slightly different. 
install from source instead.


 


Thanks in advance

 




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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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Re: [gmx-users] How to define simulation time in mdp file?

2007-09-26 Thread Mark Abraham 

Anirban Ghosh wrote:

Hi All,
Can anyone please tell me how to define simulation time in a mdp file. I 
have the following mdp file and I want to run a simulation for 50 nano 
seconds. How should I define it in this mdp file?


Section 7.3 of the GROMACS manual goes for 18 pages for a reason.

Mark
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Re: [gmx-users] installation

2007-09-26 Thread Mark Abraham 

Anupam Nath Jha wrote:

HI
try to install gromacs-3.3.1.tar.gz file. because i have installed in suse-9.3
and it's working fine.


That's because the source install doesn't pay any attention to the rpm 
database, and file conflicts such as the other user found won't be 
noticed until you go to use the mono-web package, whatever it is.


Mark
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[gmx-users] How to define simulation time in mdp file?

2007-09-26 Thread Anirban Ghosh 
Hi All,
Can anyone please tell me how to define simulation time in a mdp file. I have 
the following mdp file and I want to run a simulation for 50 nano seconds. How 
should I define it in this mdp file?

;
;User spoel (236)
;Wed Nov  3 17:12:44 1993
;Input file
;
cpp  =  /usr/bin/cpp
define  =  -DFLEX_SPC
constraints   =  none
integrator =  steep
nsteps =  1000
;
;Energy minimizing stuff
;
emtol   =  100
emstep=  0.01

nstcomm =  1
ns_type   =  grid
rlist  =  1
rcoulomb =  1.0
rvdw=  1.0
Tcoupl =  no
Pcoupl =  no
gen_vel=  no

Any suggestion is welcome.

Regards,


 
  Anirban Ghosh
  M.Tech Bioinformatics
  University of Hyderabad
  Hyderabad - 500 046
  Andhra Pradesh
  India

   
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Re: [gmx-users] installation

2007-09-26 Thread Anupam Nath Jha 
HI
try to install gromacs-3.3.1.tar.gz file. because i have installed in suse-9.3
and it's working fine.

regards
anupam


> Hi all,
>
> I am trying to install of  gromacs-3.3-1.i386.rpm in suse linux, but when I
> type:
> rpm -ivh gromacs-3.3-1.i386.rpm
>
> I get the follow error:
>
> file /usr/bin/disco from install of gromacs-3.3-1 conflicts with file from
> package mono-web-1.1.13.8-2.7
> file /usr/share/man/man1/disco.1.gz from install of gromacs-3.3-1 conflicts 
> with
> file from package mono-web-1.1.13.8-2.7
>
> I would appreciate some suggestions in this relation.
>
> Thanks in advance
>
>
>
> 
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> to amazing places on Yahoo! Travel.
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-- 
Science is facts; just as houses are made of stone, so is science is made of
facts; but a pile of stones is not a house, and  a collection of facts is not
necessarily sciece.

Anupam Nath Jha
Ph. D. Student
Saraswathi Vishveshwara Lab
Molecular Biophysics Unit
IISc,Bangalore-560012
Karnataka
Ph. no.-22932611



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Re: [gmx-users] installation

2007-09-26 Thread Mark Abraham 

Mohammad Ahmadi wrote:

Hi all,

 

I am trying to install of  gromacs-3.3-1.i386.rpm in suse linux, but 
when I type:


rpm -ivh gromacs-3.3-1.i386.rpm

 


I get the follow error:

 

file /usr/bin/disco from install of gromacs-3.3-1 conflicts with file 
from package mono-web-1.1.13.8-2.7


file /usr/share/man/man1/disco.1.gz from install of gromacs-3.3-1 
conflicts with file from package mono-web-1.1.13.8-2.7


First, find out what pacakge mono-web does and whether you can use rpm 
to uninstall it before attempting to install GROMACS. Otherwise, rpm has 
a "force install option" that will let you overwrite in such conflict cases.


Mark
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[gmx-users] installation

2007-09-26 Thread Mohammad Ahmadi 
Hi all,
 
I am trying to install of  gromacs-3.3-1.i386.rpm in suse linux, but when I 
type:
rpm -ivh gromacs-3.3-1.i386.rpm
 
I get the follow error:
 
file /usr/bin/disco from install of gromacs-3.3-1 conflicts with file from 
package mono-web-1.1.13.8-2.7
file /usr/share/man/man1/disco.1.gz from install of gromacs-3.3-1 conflicts 
with file from package mono-web-1.1.13.8-2.7
 
I would appreciate some suggestions in this relation.
 
Thanks in advance


   

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[gmx-users] the mkinl*.c and metacode.c sources

2007-09-26 Thread renying 
I am trying to build Gromacs using visual C++ with the workspace downloaded 
from ftp.gromacs.org. However the mkinl*.c and metacode.c sources, which are 
quested under '..\src\gmxlib\metacode.c', can not be found in Gromacs package. 
Whaere can I get them?




All the best

Ying  Ren
2007-09-27


State Key Laboratory of Multi-phase Complex System
Institute of Process Engineering (IPE)
Chinese Academy of Sciences (CAS)
P.O.Box 353, Beijing 100080, P.R. China
Tel: +86-10-6255 5245 ext.1
Fax: +86-10-6255 8065
http://www.ipe.ac.cn/csms/


　　
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Re: [gmx-users] make_ndx

2007-09-26 Thread Xavier Periole 

On Wed, 26 Sep 2007 20:08:06 +0100
 "Naser, Md Abu" <[EMAIL PROTECTED]> wrote:

Hi All User,

Is there anyway I can single out side chain of alpha carbon atom using 
make_ndx?


What do you mean by "single out"
and with "side chain of alpha carbon" ?



Thanks in advance.

Abu Naser 

School Of Life Sciences 
Heriot-Watt University 
Edinburgh EH14 4AS 
Email: [EMAIL PROTECTED]
Phone: +44(0)1314518265 
Fax : +44(0) 131 451 3009 







-
XAvier Periole - PhD

1- Institute of Molecular Assemblies
 City University of New York - USA
2- Molecular Dynamics-Group
 University of Groningen - The Netherlands
http://md.chem.rug.nl/~periole
-
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[gmx-users] make_ndx

2007-09-26 Thread Naser, Md Abu 
Hi All User,

Is there anyway I can single out side chain of alpha carbon atom using make_ndx?

Thanks in advance.

Abu Naser 

School Of Life Sciences 
Heriot-Watt University 
Edinburgh EH14 4AS 
Email: [EMAIL PROTECTED]
Phone: +44(0)1314518265 
Fax : +44(0) 131 451 3009 


 

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Re: [gmx-users] Recompile GROMACS

2007-09-26 Thread Yang Ye 
make shall automatically recognize the newly modified file and you just 
need to type make.
If it says nothing to do, you just need to delete the file.o of your 
modified source file and then type make.

Anyway, make clean && make will do so.

Also, if you are changing tool part, then you just need to type make 
under /src/tool, then you get the executable.

if you change part of core (grompp, mdrun)
type make under the root of the source will make them.


On 9/27/2007 12:24 AM, Rodrigo faccioli wrote:

Hi all,


I am studying GROMACS sources and I did some modifications of its 
source files. So, I would like know how do I recompile GROMACS source.


I thanks for any help.

Regards,

--
Rodrigo Antonio Faccioli
Student of Post-graduation in Electrical Engineering
University of Sao Paulo - USP
Engineering School of Sao Carlos - EESC
Department of Electrical Engineering - SEL
Intelligent System in Bioinformatics
http://laips.sel.eesc.usp.br
Phone: 55 (16) 3373-9366 Ext 229
Lattes - http://lattes.cnpq.br/1025157978990218


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Re: [gmx-users] Recompile GROMACS

2007-09-26 Thread Mark Abraham 

Rodrigo faccioli wrote:

Hi all,


I am studying GROMACS sources and I did some modifications of its source 
files. So, I would like know how do I recompile GROMACS source.


The same way you install from source :-) See the GROMACS webpage for 
general installation from source, and some links from here 
http://wiki.gromacs.org/index.php/Development for CVS info.


Mark
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[gmx-users] Recompile GROMACS

2007-09-26 Thread Rodrigo faccioli 
Hi all,


I am studying GROMACS sources and I did some modifications of its source
files. So, I would like know how do I recompile GROMACS source.

I thanks for any help.

Regards,

-- 
Rodrigo Antonio Faccioli
Student of Post-graduation in Electrical Engineering
University of Sao Paulo - USP
Engineering School of Sao Carlos - EESC
Department of Electrical Engineering - SEL
Intelligent System in Bioinformatics
http://laips.sel.eesc.usp.br
Phone: 55 (16) 3373-9366 Ext 229
Lattes - http://lattes.cnpq.br/1025157978990218
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Re: [gmx-users] Re: Pbc and Com in simulation video

2007-09-26 Thread Alan Dodd 
I believe I got as far as determining that the frame coordinates were stored in 
the rvec fr.x after being read, and passed to do_fit.  That rvec structure 
would be the key to achieving what you want, I guess.  When I got to about that 
point, I decided I could handle a little bobbing about when watching 
trajectories ;)

Alan.

- Original Message 
From: "[EMAIL PROTECTED]" <[EMAIL PROTECTED]>
To: gmx-users@gromacs.org
Sent: Wednesday, September 26, 2007 11:27:14 AM
Subject: [gmx-users] Re: Pbc and Com in simulation video


Thanks for your help Alan, Yang, and Belquis!

Now I managed to get trajectory in which a droplet stays in the middle  
of the simulation box while a surface moves below the droplet. First I  
used trjconv to remove periodicity (-pbc nojump) and then performed  
translational fit for the droplet (-fit translational) and finally  
transferred all the translating surface atoms back to the simulation  
box (-pbc -inbox).

However, there is still a problem with fitting procedure which is  
performed in three dimension and hence the surface translates upwards  
during the video. It should be quite easy to modify trjconv so that  
the fitting is performed only for the xy coordinates (not for the z  
coordinate perpendicular to the surface) but with my programming  
skills I wasn't able to do that (actually I wasnt able to find the  
correct lines). So I would like to know if someone has made a such  
modification to trjconv (trjconv_d) or could help me to do it?

Thanks,

Janne


> Hello Janne,
>
> this is what I usually do when my molecules cross the box or dance all
> around and it works for me:
>
> I first do this with the "original" unmodified or fitted xtc or trr file:
>
> trjconv -f  -o  -pbc nojump
>
> then i take the modified trr or xtc and do a fit:
>
> trjconv -f -s -fit rot+trans
>
>
> Belquis
>
>
>> Hello gmx-users!
>>
>> I am trying to make a simulation video in which a water droplet is
>> rolling or sliding on a surface. Due to a periodic boundary conditions
>> a droplet is not whole all the time but it disappears from the right
>> and appears from the left in cycles.
>>
>> I think that I could create more visual video by removing the lateral
>> motion of the center of mass of a droplet so that the droplet would
>> stay whole
>> in the middle of simulation window and the surface would translate
>> below the droplet. I am not exactly sure how realistic this kind of
>> video would be and would like to know if someone has better ideas?
>>
>> If there are no better ideas I would need advices to be able to create
>> a such trajectory or video. Right now I am struggling with trjconv
>> which might be suitable for this purpose. However, if I use the
>> droplet as a group for translational fit (-fit translation) I get
>> trajectory in which the whole system wanders strangly (laterally (the
>> surface moves first to the left and then back to the right) and also
>> in perpendicular to the surface due to the lowering of the height of
>> the center of mass of the droplet during the simulation) and the
>> droplet wont stay whole in the middle of the box. Any ideas what I am
>> doing wrong or how I would be able to get rid of even this lateral
>> wandering so that I could at least see how realistic this procedure is?
>>
>>
>> Thanks for your time and help in advance,
>>
>> Janne
>>
>>
>> --
>> Janne Hirvi, MSc(Physical Chemistry), Researcher
>> University of Joensuu, Department of Chemistry, P.O.Box 111 80101 Joensuu,
>> FI
>> Tel: +358 13 2514544 & +358 50 3474223
>> E-mail: [EMAIL PROTECTED] & [EMAIL PROTECTED]
>> --
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[gmx-users] Re: Pbc and Com in simulation video

2007-09-26 Thread janne . hirvi 

Thanks for your help Alan, Yang, and Belquis!

Now I managed to get trajectory in which a droplet stays in the middle  
of the simulation box while a surface moves below the droplet. First I  
used trjconv to remove periodicity (-pbc nojump) and then performed  
translational fit for the droplet (-fit translational) and finally  
transferred all the translating surface atoms back to the simulation  
box (-pbc -inbox).


However, there is still a problem with fitting procedure which is  
performed in three dimension and hence the surface translates upwards  
during the video. It should be quite easy to modify trjconv so that  
the fitting is performed only for the xy coordinates (not for the z  
coordinate perpendicular to the surface) but with my programming  
skills I wasn't able to do that (actually I wasnt able to find the  
correct lines). So I would like to know if someone has made a such  
modification to trjconv (trjconv_d) or could help me to do it?


Thanks,

Janne



Hello Janne,

this is what I usually do when my molecules cross the box or dance all
around and it works for me:

I first do this with the "original" unmodified or fitted xtc or trr file:

trjconv -f  -o  -pbc nojump

then i take the modified trr or xtc and do a fit:

trjconv -f -s -fit rot+trans


Belquis



Hello gmx-users!

I am trying to make a simulation video in which a water droplet is
rolling or sliding on a surface. Due to a periodic boundary conditions
a droplet is not whole all the time but it disappears from the right
and appears from the left in cycles.

I think that I could create more visual video by removing the lateral
motion of the center of mass of a droplet so that the droplet would
stay whole
in the middle of simulation window and the surface would translate
below the droplet. I am not exactly sure how realistic this kind of
video would be and would like to know if someone has better ideas?

If there are no better ideas I would need advices to be able to create
a such trajectory or video. Right now I am struggling with trjconv
which might be suitable for this purpose. However, if I use the
droplet as a group for translational fit (-fit translation) I get
trajectory in which the whole system wanders strangly (laterally (the
surface moves first to the left and then back to the right) and also
in perpendicular to the surface due to the lowering of the height of
the center of mass of the droplet during the simulation) and the
droplet wont stay whole in the middle of the box. Any ideas what I am
doing wrong or how I would be able to get rid of even this lateral
wandering so that I could at least see how realistic this procedure is?


Thanks for your time and help in advance,

Janne


--
Janne Hirvi, MSc(Physical Chemistry), Researcher
University of Joensuu, Department of Chemistry, P.O.Box 111 80101 Joensuu,
FI
Tel: +358 13 2514544 & +358 50 3474223
E-mail: [EMAIL PROTECTED] & [EMAIL PROTECTED]
--

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RE: [gmx-users] HIV protease dimer Energy minimization-ERROR

2007-09-26 Thread serdar durdagi 
Dear Karunakaran,
   
  I don't think there is any error here.
   
  I have also made MD simulations of HIV-PR dimer with Gromacs, but I couldn't 
observed complete seperation of dimer to monomers. It seems after 1ns 
simulation, there is a seperation between tips of flaps. (I mean the seperation 
between Gly49, Ile50, Gly51 and Gly49', Ile50', Gly51').I measured about 5 
Angstrom seperation (average), distance between the alpha carbon atoms for 
these residues after simulation. 
   
  When you put some inhibitors to this cavity, this seperation may restricted.
   
  You may check the article: Schuster et al, Biochemistry, 42, 1326, 2003.
   
   
  Serdar Durdagi
   
   
   
  

chandran karunakaran <[EMAIL PROTECTED]> schrieb:
  Dear GMX users,

On running the MD for HIV protease as dimer
structure, it gets separated after the energy
minimization. (That’s dimer is separated into two
monomers). 

Could you kindly help me out in running HIV
protease as dimer? 

with thanks
c.karunakaran


***+ 
Dr.Karunakaran Chandran +
Biophysics Department + 
Medical College of Wisconsin +
Milwaukee, WI-53226 +
Resi.: 414-443-0085 +
Off : 414-456-4034 +





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