[gmx-users] editconf

[Payman Pirzadeh]

After rotation, wouldn't a minimization with very very small steps solve the
problem?

Paymon

-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Mark Abraham
Sent: October 18, 2010 7:14 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] editconf

  On 19/10/2010 8:11 AM, Paymon Pirzadeh wrote:
> Hello,
> I am trying to rotate my protein in my simulation box (solvent molecules
> are there as well). I issue the following command:
>   editconf_d_mpi -f AFPIII_Ih0001_54_26_em.gro -n protein.ndx -rotate 15
> 180 0 -o AFPIII_Ih0001_54_26_rotated.gro -box 5.40022 6.23564 20.59328
>
> I select my group (protein) in the first group selection prompt and
> whole system as output in the second prompt. However, in the output file
> the whole system is rotated rather than protein only. Also, despite the
> -box switch used, the dimensions of the box changes.
> Is there any ideas on what I am missing in my procedure?

editconf can't rotate the solute with solvent present - what would you 
like it to do about the voids and clashes that would be created? Do your 
rotation before you solvate.

Mark
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