[gmx-users] Problems in the modelling of interaction between peptide and copper

Alex nedomacho at gmail.com
Thu Apr 23 09:20:42 CEST 2015

Also, I assumed by "copper" you meant an actual surface of copper, not
a few copper ions floating in water. :)


MT> Dear all,

MT> I got a problem when modelling the interaction of a peptide and
MT> copper. I am using the force field of opls-aa. The charge of
MT> copper atoms are defined as zero and the non-bonded parameters are
MT> obtained from the CU ions, which can be
MT> found in opls-aa.

MT> I applied smd and found that the peptide is approaching the
MT> copper surface and stopped when it is very close to the surface,
MT> due to some abnormal interaction. The whole process seems quite
MT> reasonable, however, when I rerun the
MT> simulation to obtain the interaction energy, for the vdw
MT> interaction between peptide and copper is zero, absolute zero, in the whole process.

MT> Can anyone give me some suggestions? Is my model reasonable? I am
MT> not so confident with modelling strategy of using the LJ
MT> parameters for copper bulk material. Also the zero interaction energy is another big issue.

MT> Cheers,
MT> Tng

Best regards,
 Alex                            mailto:nedomacho at gmail.com

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