Re: Error in Minimization

From: Axel Kohlmeyer (
Date: Tue Nov 10 2009 - 13:30:10 CST

On Mon, 2009-11-09 at 22:19 -0500, Ale Gomez wrote:

dear ale,

> Thanks Axel for your great answer.

> I am not sure about the "complex protocol" that you told me. My first
> step was keeping protein fix and then try to minimize the system but I
> had the same values. Then I fixed the membrane and ran minimize, but
> still doesn't work. Perhaps my system is too complex for this
> procedure that I must do something else??? If I am right, could you
> explain me what exactly should I do??

> When I prepared my system, I visualized it with VMD and seems like
> there is
> not overlapping at all. What you think must be a correct separation
i am by far not an expert in this. i mostly relayed what i learned
from (former) people in our group that have/had extensive experience
in running peptide in lipid bilayer systems.

from what you describe it looks like some part of your system does have
overlap. when you checked in VMD, have you considered PBC? you have
to make your simulation box also large enough, but at the same time
make sure is "heals" well.

you should perhaps split your system into segments and try to minimize
each of them separately. not to use the result, but to identify where
the problematic structure lies. if all of them run well, then you can
put the system back together piece by piece and see at which segment
addition it goes haywire.


> for my
> protein in the membrane??, now I set up it with 9 angstroms.
> Thanks in advance for all your help.
> -------------------------------------------------------------------
> Ale Gomez
> Biophysics and Molecular Modelling Group
> Physics Department
> Escuela Politecnica Nacional, Quito-Ecuador
> Ladron de Guevara E11-253.
> Phone: 593-95292408

Dr. Axel Kohlmeyer 
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.

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