[gmx-users] editconf

Mark Abraham Mark.Abraham at anu.edu.au
Tue Oct 19 03:26:04 CEST 2010

  On 19/10/2010 12:22 PM, Payman Pirzadeh wrote:
> After rotation, wouldn't a minimization with very very small steps solve the
> problem?

Only if the solute surface was very close to being symmetric about the 
rotation axis. Since that never happens, editconf doesn't even have the 
ability to try.

> 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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