[gmx-users] free energy calculations for reference state for constant pH MD simulations...

bipin singh bipinelmat at gmail.com
Tue Jan 28 08:46:16 CET 2014

See the section  "5.7.4 Topologies for free energy calculations" in Gromacs
4.6.5 manual.

On Tue, Jan 28, 2014 at 3:09 AM, Ozbil, Mehmet <m.ozbil at umiami.edu> wrote:

> Hello,
> I am trying to run constant pH MD with GROMACS, and started with the TI
> free energy calculations. I am following Justin Lemkul`s free energy
> calculation tutorial, and assuming that the free energy calculations will
> be similar to calculate the protonation energy of titratable amino acids
> such as GLU or HIS.
> My question is that, while scanning the lambda values for the free energy
> calculations do I need to define both protonated and deprotonated states of
> GLU in the same .top and .pdb file, or I just use one .top and one .pdb
> file and by changing the lambda values from 0.0 to 1.0 it does the
> deprotonation itself. If I need to incorporate the two states in one .top
> and .pdb file can anyone help with how to do that?
> Thanks,
> Mehmet Ozbil
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*--------------------Thanks and Regards,Bipin Singh*

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