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

From: Brian Radak (brian.radak_at_gmail.com)
Date: Fri May 04 2018 - 15:46:56 CDT

I mean what were the options you gave to ParseFEP? It would also be useful
to see portions of the output which summarize the data.

On Fri, May 4, 2018, 4:00 PM Francesco Pietra <chiendarret_at_gmail.com> wrote:

> 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
>>>>>
>>>>>
>>>>
>>>
>>
>

This archive was generated by hypermail 2.1.6 : Sat Sep 14 2019 - 23:19:30 CDT