<P>>On Wed, 2004-11-24 at 07:03 +0000, Maarten Wolf >wrote:<BR>>> Hello,<BR>>> <BR>>> I am doing md simulations on a small peptide in water.<BR>>> These calculations result in a consistent salt bridge on the surface<BR>>> of the protein. <BR>>> I find this strange, because I allways thought that salt-bridges on<BR>>> the surface are easily solvated, and thus broken.<BR>>> Is this assumption wrong? Or is this force field related? Or something<BR>>> else? <BR>>The assumption is wrong in the sense the some >saltbridges are stable and<BR>>others aren't. It may have to do with many things, e.g. a >Lys has quite<BR>>a long hydrophobic that likes being packed. Can also >be force field<BR>>related, or to the size of your box or the amount of >counterions...</P>
<P>How might the box size effect the stability of the salt bridge? </P>
<P>I performed another simulation with a lot of counterions. The whole protein structure changed, but the salt bridge remained there. Can I then say that the protein structure and the number of counterions have nothing to do with it?<BR></P>
<P>>> <BR>>> Thanks for any help in advance<BR></P>
<P>>> <BR>>> <BR>>> MvG Maarten<BR>>> <BR>>> ******************************************************<BR>>> ** Work Adress Julianalaan 136 ** <BR>>> ** 2628 BL Delft **<BR>>> ** Netherlands **<BR>>> ** +31(0)15-2789382 **<BR>>> ******************************************************<BR>>> <BR>>> <BR>>> >______________________________________________________________________<BR>>> ALL-NEW Yahoo! Messenger - all new features - >even more fun! <BR>>> >_______________________________________________<BR>>> gmx-users mailing list<BR>>> <A href="http://uk.f257.mail.yahoo.com/ym/Compose?To=gmx-users@gromacs.org&YY=53937&order=down&sort=date"><FONT color=#003399>gmx-users@gromacs.org</FONT></A><BR>>> <A href="http://www.gromacs.org/mailman/listinfo/gmx-users" target=_blank><FONT color=#003399>http://www.gromacs.org/mailman/listinfo/gmx-users</FONT></A><BR>>>
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