[gmx-users] Drug alone again

Tanos C. C. França tccf at epq.ime.eb.br
Mon Jun 9 19:43:00 CEST 2003

      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 ??????
      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

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