[gmx-users] Minimization in vacuo

[Fabrizio Mancinelli]

Hi IBB,

the answer to your question depends on the precision grade you want to reach.
If you want to properly minimize (for example a normal modes analysis), you 
should use double precision version of the software (ask your system 
administrator) and an emtol of about 10e-04 or even less.

Fabrizio

Alle 11:16, giovedì 23 febbraio 2006, Mahnam ha scritto:
> In the name of God
> Hello dear Tsjerk A. Wassenaar
> Tanke you very much for your guide. I want to do only energy
> minimization and not MD after it.Must I use  ffG43b1 and emtol for cg
> lesser of emtol for steep .? When do we must use ffG43b1.?
> Thank you very much in advance
> Institute of  Biochemistry  and  Biophysics (IBB)
> Tehran University
> P.O.box 1417614411
> Tehran
> Iran
>
>
>
>
> -----Original Message-----
> From: "Tsjerk Wassenaar" <tsjerkw at gmail.com>
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Date: Thu, 23 Feb 2006 11:02:25 +0100
> Subject: Re: [gmx-users] Minimization in vacuo
>
>
> Hi Institute of Biochemistry and Biophysics (or can I say IBB? :) ),
>
>
> On 2/23/06, Mahnam < mahnam at ibb.ut.ac.ir > wrote:
>
>
> In the name of God
> Hello gmx users :
> I want to do energy minimization in vacuo .Must I select ffG43b1 and
> emtol for cg lesser of emtol for steep similar to " GROMACS Tutorial for
> Drug ? Enzyme Complex ".?
>
>
> If you're going to do a simulation afterwards in solution, don't bother.
> ffG43b1 is for running simulations in vacuum, energy minimization is
> just to get rid of these bad contacts in the structure.
>
>
>
> Thank you very much in advance
> Institute of  Biochemistry  and  Biophysics (IBB)
> Tehran University
> P.O.box 1417614411
> Tehran
> Iran
>
>
>
> And talking about nettiquette.., please sign your posts. That way, we
> know just that bit more about who we're dealing with and how to address
> you.
>
> Cheers,
>
> Tsjerk