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.
-Justin
Paymon
-----Original Message-----
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@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
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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