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

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Fri May 04 2018 - 10:51:45 CDT

VMD 1.9.4a12

ParseFEP was provided to me fro Dr Chris Chipot on last Mar 8.
>From that:
# Chris Chipot, Liu Peng, 2007-2012
# INCLUSION OF PARSER. MAY 28, 2009, C.C.
# 1.8 2013-12-20
#----------------------------------------------------------------------
# $Id: parseFEP.tcl,v 1.14 2014/12/10 16:08:57 johns Exp $
#----------------------------------------------------------------------
# YingChih Chiang (Letitia), 2017/01/18, 2017/11/20
# Re-structure the source code for performance:
# (1) Reading fepout files are done via calling readfepout.
# (2) Only read the fepout files once and save the data.
# (3) Bugs of reading fepout files in BAR_estimator and
# inaccuracy_estimation have been removed.
# YingChih Chiang (Letitia), 2018/02/01, 2018/02/10

francesco

On Fri, May 4, 2018 at 3:01 PM, Brian Radak <brian.radak_at_gmail.com> wrote:

> 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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