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

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Fri May 04 2018 - 15:00:22 CDT

The VMD forum was omitted to avoid irritating some folks (I am not
referring to Alice Cooper's nightmare).

The calculation for the Unbound was carried out as I described:

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

using the layout of the .namd input files as in the tutorial. Should that
be not enough, please instruct me how to satisfy your request.

thanks

francesco

On Fri, May 4, 2018 at 6:04 PM, Brian Radak <brian.radak_at_gmail.com> wrote:

> 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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