Re: Fixed COM

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Tue Jul 12 2011 - 08:11:04 CDT

Hi,

Thank you for your prompt reply. As I want to calculate free energy of
> solvation of this molecule (the fixed one) by means of FEP method, does this
> restrain affects FEP results?
>

That is difficult to say. Why do you want to restrict the COM anyway? If you
have periodic boundary conditions and just a protein in solution there is no
need to restrict the COM.
I'm not very familiar with FEP, but if the restrains are similar before and
after the solvation then using colvars should not effect the outcome of the
calculation. But since the diffusion in water and in vacuum is
probably different I'm not 100% sure this is the case.

Perhaps somebody with more experience with using FEP could clarify?

Best regards,
Ajasja

PS: It is customary to keep the namd mailing list in the cc, so that others
can potentially benefit from the problem's resolution.

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