Re: vmd-l: Fwd: FEP with intermediary segments

From: Brian Radak (brian.radak_at_gmail.com)
Date: Fri May 04 2018 - 08:01:28 CDT

This sounds like a question regarding ParseFEP. Can you be more specific
about:

- which version of ParseFEP/VMD you are using?
- what options you used (I presume from the GUI, not the terminal)?

On Fri, May 4, 2018 at 1:37 AM, Francesco Pietra <chiendarret_at_gmail.com>
wrote:

> Perhaps this question about "FEP with Intermediary Segmants" has passed
> unnoticed.
> thanks
> for paying attention to
>
> fp
> ---------- Forwarded message ----------
> From: Francesco Pietra <chiendarret_at_gmail.com>
> Date: Thu, Apr 26, 2018 at 5:20 PM
> Subject: FEP with intermediary segments
> To: NAMD <namd-l_at_ks.uiuc.edu>, VMD Mailing List <vmd-l_at_ks.uiuc.edu>
>
>
> Hello:
> For the Unbound ligand, in the frame of ligand-receptor FEP, I carried
> out, formally successfully, the following segment of the Hamiltonian steep
> region
>
> frwd 0.00 0.20 0.05
> back 0.20 0.00 -0.05
>
> using preeq 1ns, FEP 6ns, and I/O outputs 2000
>
> Because of scalability problems, I have now divided the remaining region
> in two sectors.
> For the 0.2-0.6 sector:
>
> frwd 0.20 0.60 0.1
> back 0.60 0.20 -0.1
>
> ParseFEP gave only a log file with tables for
> Free energy perturbation
> Inaccuracy
> perturbation theory
>
> NO graphic outputs and no useful warning
>
> Was the setting up of the FEP incorrect, or intermediary sectors can not
> be used?
>
> Thanks for advice
> francesco pietra
>
>

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