[gmx-users] Steered MD

[chandran karunakaran]

HI GMX users,

   I am interested in SMD using GMX.
Does any body help me in giving the 
sample necessary files for running
SMD in GMX? Thanks so much in advance. 

With thanks
Dr.C.Karunakaran


--- gmx-users-request at gromacs.org wrote:

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> Today's Topics:
> 
>    1. installing GROMACS3.3 using RPM packages for
> Linux
>       (lsettimo at abo.fi)
>    2. Re: installing GROMACS3.3 using RPM packages
> for Linux
>       (lsettimo at abo.fi)
>    3. gromacs3.3 problem after installation  (Wang
> Zhun)
>    4. Re: gromacs3.3 problem after installation 
> (Erik Lindahl)
>    5. Re: Re: installing GROMACS3.3 using RPM
> packages for Linux
>       (Erik Lindahl)
>    6. Re: LINCS error with 3.3 (Yang Ye)
>    7. Re: Discrepancy between Free Energy
> Perturbation using
>       Gromos96 and OPLS (Erik Lindahl)
> 
> 
>
----------------------------------------------------------------------
> 
> Message: 1
> Date: Wed, 12 Oct 2005 19:24:03 +0300
> From: lsettimo at abo.fi
> Subject: [gmx-users] installing GROMACS3.3 using RPM
> packages for
> 	Linux
> To: gmx-users at gromacs.org
> Message-ID:
> <1129134243.434d38a304e2e at webmail.abo.fi>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Dear all,
> I would like to install GROMACS 3.3 using RPM
> packages for Linux.
> I am running a x86_64 system and using Fedora Core 4
> (x86_64).
> 
> When I unpack the rpm, I get the complaint regarding
> FFTW dependencies
> (it needs libfftw3f.so.3).
> 
> Since something very similar has already occured in
> the past:
>
http://www.gromacs.org/pipermail/gmx-users/2004-June/011053.html
> 
> I followed the same instructions given by Erik
> Lindahl unpacking
> gromacs-3.3-1.src.rpm.
> 
> 
> When I rebuild rpmbuild -bb gromacs.spec in
> /usr/src/redhat/SPECS
> it complains that:
> 
> error: Legacy syntax is unsupported: copyright
> error: line 14: Unknown tag: Copyright: GPL
> 
> Does anybody know what these messages means?
> Any file is created after this commmand (the
> directory 
> /usr/src/redhat/RPMS/x86_64/ is empty).
> 
> Thanks if somebody will help me.
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Wed, 12 Oct 2005 19:36:36 +0300
> From: lsettimo at abo.fi
> Subject: [gmx-users] Re: installing GROMACS3.3 using
> RPM packages for
> 	Linux
> To: gmx-users at gromacs.org
> Message-ID:
> <1129134996.434d3b94a605b at webmail.abo.fi>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Ignore my previous email. I solved the problem.
> 
> > Dear all,
> > I would like to install GROMACS 3.3 using RPM
> packages for Linux.
> > I am running a x86_64 system and using Fedora Core
> 4 (x86_64).
> > 
> > When I unpack the rpm, I get the complaint
> regarding FFTW
> > dependencies
> > (it needs libfftw3f.so.3).
> > 
> > Since something very similar has already occured
> in the past:
> >
>
http://www.gromacs.org/pipermail/gmx-users/2004-June/011053.html
> 
> > I followed the same instructions given by Erik
> Lindahl unpacking
> > gromacs-3.3-1.src.rpm.
> > 
> > 
> > When I rebuild rpmbuild -bb gromacs.spec in
> /usr/src/redhat/SPECS
> > it complains that:
> > 
> > error: Legacy syntax is unsupported: copyright
> > error: line 14: Unknown tag: Copyright: GPL
> > 
> > Does anybody know what these messages means?
> > Any file is created after this commmand (the
> directory 
> > /usr/src/redhat/RPMS/x86_64/ is empty).
> > 
> > Thanks if somebody will help me.
> 
> 
> 
> 
> ------------------------------
> 
> Message: 3
> Date: Thu, 13 Oct 2005 01:35:55 +0800
> From: Wang Zhun <wangzhun at pumc.edu.cn>
> Subject: [gmx-users] gromacs3.3 problem after
> installation 
> To: gmx-users at gromacs.org
> Message-ID: <329139263.14925 at pumc.edu.cn>
> Content-Type: text/plain; charset=ISO-8859-1;
> format=flowed
> 
> Hi,
> I've installed version 3.3 but failed to get it
> work.
> Eg: pdb2gmx is in my path but cannot be found, and 
> segmentation fault 
> will occur if it's carried out.
> I don't know what's the problem.
> 
> 
> [wzh at hewei wzh]$ pdb2gmx -h
> tmpstrtrp[i]tmpstrtrp[i]tmpstrtra and K. 
>
Nemototmpstrtrtmpstrtrtmpstrtrtmpstrtrtmpstrtrtmpstrtrtmpstrtrtmpstrtrp[i]tmpstrtrp[i]t
> 
> of range 
>
(135930989)------------------------------------------------------------
> No filetype (null)
> d argument rint help info for option
> (null)Segmentation fault
> [wzh at hewei wzh]$ whereis pdb2gmx
> pdb2gmx:
> [wzh at hewei wzh]$ ls /usr/local/gromacs/bin/pdb2gmx
> /usr/local/gromacs/bin/pdb2gmx*
> [wzh at hewei wzh]$ echo $PATH
>
/usr/local/bin:/bin:/usr/bin:/usr/X11R6/bin:/usr/games:/usr/X11R6/bin:/usr/games:/usr/X11R6/bin:/usr/games:/usr/X11R6/bin:/usr/games:.:/usr/X11R6/bin:/usr/games:/usr/local/gromacs/bin:/home/wzh/biolinux/autodock/bin:/home/wzh/bin
> [wzh at hewei wzh]$  /usr/local/gromacs/bin/pdb2gmx
> tmpstrtrp[i]tmpstrtrp[i]tmpstrtra and K. 
>
Nemototmpstrtrtmpstrtrtmpstrtrtmpstrtrtmpstrtrtmpstrtrtmpstrtrtmpstrtrp[i]tmpstrtrp[i]t
> 
> of range 
>
(135930989)------------------------------------------------------------
> No filetype (null)
> d argument rint help info for option
> (null)Segmentation fault
> 
> 
> ------------------------------
> 
> Message: 4
> Date: Wed, 12 Oct 2005 19:56:41 +0200
> From: Erik Lindahl <lindahl at sbc.su.se>
> Subject: Re: [gmx-users] gromacs3.3 problem after
> installation 
> To: Discussion list for GROMACS users
> <gmx-users at gromacs.org>
> Message-ID:
> <39D6D7A3-997E-40B9-9D71-54BA3D1DC6CC at sbc.su.se>
> Content-Type: text/plain; charset=US-ASCII;
> delsp=yes; format=flowed
> 
> Hi,
> 
=== message truncated ===



	
		
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