[gmx-users] RE GROMAC Free Energy Question on Topologies

hannes.loeffler at stfc.ac.uk hannes.loeffler at stfc.ac.uk
Wed May 4 22:01:22 CEST 2016

I suggest to keep all discussions on the mailing list for the benefit of others.

The masses are recommended to keep at one end state primarily to avoid bad interactions with constraints that may be involved in the transformation.  In a thermodynamical cycle contributions from the masses should fully cancel anyway.

From: Billy Williams-Noonan [billy.williams-noonan at monash.edu]
Sent: 04 May 2016 11:31
To: Loeffler, Hannes (STFC,DL,SC)
Subject: RE GROMAC Free Energy Question on Topologies

Hi Hannes.

Thank you for answering my question on GROMACS - I'm having trouble using the mailing list system and it's easier for me to e-mail you... I hope you don't mind.

You said that I should not 'annihilate' bonded terms for dummy atoms and referred me to some relevant papers by Boresch, which I'll read tonight...

Should I also keep the masses of perturbed atoms the same or alter them with thew FEP lambdas setting?  I thought it would be easier to quickly ask you than scroll through the archives...

Thanks again for your help...


Billy Noonan    |    PhD Student    |    Bsci ( Adv ), IA Hon

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