[gmx-users] Drug alone again

[David]

On Mon, 2003-06-09 at 19:41, Tanos C. C. França wrote:
>       Dear Daan,
> 
>       Ok, But I need to perform a em of my drug in a water box and,
> then, a MD. How can I do this with the drug alone ???? Is that
> possible in GROMACS ??????
of course when you have a topology.

just follow the gromacs tutorial but replace the speptide by your drug
molecule.
> 
>       Thanks in advance.
> 
>       Tanos C. C. França
> 
>       IME – Rio de Janeiro - Brazil
> 
>  
> 
>  
> 
> Message: 2
> 
> Date: Sun, 8 Jun 2003 11:26:21 +0100 (BST)
> 
> From: Daan van Aalten <vdava at davapc1.bioch.dundee.ac.uk>
> 
> To: "=?iso-8859-1?Q?Tanos_C._C._Fran=E7a?=" <tccf at epq.ime.eb.br>
> 
> cc: <gmx-users at gromacs.org>
> 
> Subject: Re: [gmx-users] Minimization of a drug alone
> 
> Reply-To: gmx-users at gromacs.org
> 
>  
> 
>  
> 
> Dear Tanos
> 
>  
> 
> The PRODRG server by default run a GROMACS EM on your compound
> 
>  
> 
> these are the GMX grompp input file that the server uses:
> 
>  
> 
>  
> 
>  cpp                 =3D  /lib/cpp
> 
>  define              =3D  -DFLEX_SPC
> 
>  constraints         =3D none
> 
>  integrator          =3D steep
> 
>  nsteps              =3D  50000
> 
>  ;
> 
>  ;      Energy minimizing stuff
> 
>  ;
> 
>  emtol               =3D  1
> 
>  emstep              =3D  0.01
> 
>  
> 
>  nstcomm             =3D  1
> 
>  ns_type             =3D  grid
> 
>  rlist               =3D  1
> 
>  rcoulomb            =3D 1.0
> 
>  rvdw                =3D  1.0
> 
>  Tcoupl              =3D  no
> 
>  Pcoupl              =3D  no
> 
>  gen_vel             =3D  no
> 
>  pbc                 =3D  no
> 
>  
> 
>  
> 
>  
> 
> cheers
> 
>  
> 
> Daan
> 
>  
> 
> 
> ---
> Outgoing mail is certified Virus Free.
> Checked by AVG anti-virus system (http://www.grisoft.com).
> Version: 6.0.488 / Virus Database: 287 - Release Date: 05/06/2003
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++