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

From: Brian Radak (brian.radak_at_gmail.com)
Date: Fri May 04 2018 - 11:04:10 CDT

That's step one - how did you run your calculation?

On Fri, May 4, 2018 at 11:51 AM, Francesco Pietra <chiendarret_at_gmail.com>
wrote:

> 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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