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
- 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>
> Perhaps this question about "FEP with Intermediary Segmants" has passed
> for paying attention to
> ---------- 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>
> For the Unbound ligand, in the frame of ligand-receptor FEP, I carried
> out, formally successfully, the following segment of the Hamiltonian steep
> 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
> 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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