[gmx-users] query about diferent cutoffs

Ragothaman Yennamalli ymr79in at yahoo.co.in
Wed Apr 9 19:29:48 CEST 2008

Dear all,
In a particular setup of a protein interacting with
ions, the protein needs to be simulated without ions
and after a certain point of time the ions are
introduced to the system, so as to check of the
protein undergoes refolding in the presence ions or
not. Since it is a known fact that in the absence of
ions protein undergoes conformational change and in
the presence of ions the protein remains stable. 

My question is: Can two different distance cutoffs be
defined in gromacs? for eg The distance range for
protein and ions not more than 20Angstroms and for
solvent-solvent not more than 8Angstroms.

Thanks in advance,


Y. M. Ragothaman,
Research Scholar,
Centre for Computational Biology and Bioinformatics,
School of Information Technology,
Jawaharlal Nehru University,
New Delhi - 110067.

Telephone: 91-11-26717568, 26717585
Facsimile: 91-11-26717586

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