[gmx-users] editconf

Justin A. Lemkul jalemkul at vt.edu
Tue Oct 19 03:23:52 CEST 2010

Payman Pirzadeh wrote:
> After rotation, wouldn't a minimization with very very small steps solve the
> problem?

If any atoms overlap, you can't count on this working.  It would be hit or miss. 
  The proper way to build the system would be to orient the solute, then fill 
the box with solvent.  Far more reliable.


> 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


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list