[gmx-users] Steered MD

Thu Oct 13 16:07:53 CEST 2005

I'm new to this mailing list but there was another
question about SMD here about a year ago and I'm
afraid none answered it so I guess you could contact
Martinez et. al, which, if I'm not mistaken, recently
did a work using SMD: "Molecular dynamics simulations
reveal multiple pathways of ligand dissociation from
thyroid hormone receptors".
Rodrigo S. Reston, BSc.
UFMG, Brazil.

--- chandran karunakaran <ckaru2000 at yahoo.com> wrote:

> 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:
> 
> > Send gmx-users mailing list submissions to
> > 	gmx-users at gromacs.org
> > 
> > To subscribe or unsubscribe via the World Wide
> Web,
> > visit
> > 	http://www.gromacs.org/mailman/listinfo/gmx-users
> > or, via email, send a message with subject or body
> > 'help' to
> > 	gmx-users-request at gromacs.org
> > 
> > You can reach the person managing the list at
> > 	gmx-users-owner at gromacs.org
> > 
> > When replying, please edit your Subject line so it
> > is more specific
> > than "Re: Contents of gmx-users digest..."
> > 
> > 
> > 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 ===
> 
> 
> 
> 	
> 		
> __________________________________ 
> Yahoo! Mail - PC Magazine Editors' Choice 2005 
> http://mail.yahoo.com
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the
> list. Use the
> www interface or send it to
> gmx-users-request at gromacs.org.
> 

__________________________________ 
Yahoo! Mail - PC Magazine Editors' Choice 2005 
http://mail.yahoo.com