ppirzade at ucalgary.ca
Tue Oct 19 04:03:16 CEST 2010
Dear Mark and Justin,
Thanks for very informative comments. I'll try to rotate and then solvate.
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Mark Abraham
Sent: October 18, 2010 7:26 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] editconf
On 19/10/2010 12:22 PM, Payman Pirzadeh wrote:
> After rotation, wouldn't a minimization with very very small steps solve
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.
> -----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:
>> 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.
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