**From:** Bhati, Agastya (*agastya.bhati.14_at_ucl.ac.uk*)

**Date:** Wed Oct 11 2017 - 14:50:46 CDT

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Hi Chitrak,

Thanks for the prompt reply.

I am performing FEP/REST2 simulations here (http://www.pnas.org/content/109/6/1937.full), where each replica has a different REST2 scaling factor (\sptscale) as well as alchemical paramater (\lambda) and exchanges are attempted between them. The problematic conformations I am referring to here are the ones where an alchemically transforming atom has very close contact with some other atom from rest of the system. This leads to very high values of potential energies and potential derivatives wrt \lambda. Well-behaved in this case means that no such bad contacts are observed in any of the snapshots of the sorted trajectories.

Such contacts, in my understanding, can occur only when somehow due to incorrect sorting, the conformations from end-points states (\lambda =0 or 1) end up in one of the intermediate states.

Hope that helps. Let me know if you need more clarification.

Regards,

Agastya

________________________________

From: Chitrak Gupta <chgupta_at_mix.wvu.edu>

Sent: 11 October 2017 20:32:54

To: NAMD list; Bhati, Agastya

Subject: Re: namd-l: Implementation of sortreplicas executable for restarted REST2 simulations

Hi Agastya,

I have not done FEP but have used the REST2 version you referred to. Could you elaborate why you mean by "well-behaved" and what problem you had in your case 2?

Chitrak.

On Wed, Oct 11, 2017 at 3:12 PM, Bhati, Agastya <agastya.bhati.14_at_ucl.ac.uk<mailto:agastya.bhati.14_at_ucl.ac.uk>> wrote:

Hi,

I have been performing FEP/REST2 simulations using the customised NAMD developed by Sunhwan and Wei (https://doi.org/10.1016/j.cpc.2015.08.030

Agastya

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