[gmx-users] DMSO, counter ions and ionization state

[Edgar Luttmann]

Dear all,

does anyone have experiences with the treatment of charges during 
peptide simulations in DMSO?

The pka of the sidechains as well as the termini might be significantly 
different in DMSO than water and thus I wonder if there is a convenient 
way to estimate the ionization state of the residues. Furthermore would 
you just put counter ions into the DMSO - or would you keep the peptide 
neutral?

Any suggestions are welcome and thanks in advance..

Edgar

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Dr. Edgar Luttmann
Max-Planck-Institute for Biophysical Chemistry
Department 070 - Theoretical and Computational Biophysics Group

Am Fassberg 11, 37077 Goettingen, Germany
Tel: +49 551 201-2320, Fax: +49 551 201-2302
E-Mail: edgar.luttmann( at )mpi-bpc.mpg.de / eluttma( at )gwdg.de
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