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

**Date:** Thu Oct 12 2017 - 09:00:27 CDT

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I can't think of any way to confirm if the sorting is correct or not in case of REST2 simulations. Since, in such calculations, the Hamiltonian of a given replica does not vary much from those of others, the results only vary slightly even in case of incorrect sorting. However, comparing the results after sorting with and without extra snapshot can hint towards that. For instance, in my case, I find that results are more accurate after sorting the trajectories with an extra snapshot. In addition, the distribution of energies and energy derivatives is wider on sorting without an extra snapshot.

Agastya

________________________________

From: Chitrak Gupta <chgupta_at_mix.wvu.edu>

Sent: 12 October 2017 14:21:09

To: Bhati, Agastya

Cc: NAMD list

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

Ok, so here is my question. In the absence of a FEP-coupling, how do you know whether or not the sorting was correct?

On Thu, Oct 12, 2017 at 7:50 AM, Bhati, Agastya <agastya.bhati.14_at_ucl.ac.uk<mailto:agastya.bhati.14_at_ucl.ac.uk>> wrote:

The same thing also seems to happen for my REST2 (not coupled to FEP) simulations (as the same sortreplicas executable is used for sorting in both type of calculations). However, in that case there is no chance of such close contacts occurring, and hence, the problem is not immediately obvious. So, after I observed this problem in FEP/REST2 simulations, I tried to sort the REST2 trajectories again by adding a frame at the beginning of the original unsorted trajectories. This improved my results slightly!

May be you wanna give it a go?

Regards,

Agastya

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From: Chitrak Gupta <chgupta_at_mix.wvu.edu<mailto:chgupta_at_mix.wvu.edu>>

Sent: 12 October 2017 02:20:24

To: Bhati, Agastya

Cc: NAMD list

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

Ah, I see.

I have only used REST2 just by itself (i.e. no FEP coupled to it). Maybe someone who has done this could provide a good exaplanation.

Chitrak.

On Wed, Oct 11, 2017 at 3:50 PM, Bhati, Agastya <agastya.bhati.14_at_ucl.ac.uk<mailto:agastya.bhati.14_at_ucl.ac.uk>> wrote:

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<mailto: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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