VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri May 04 2018 - 11:12:04 CDT

folks, please stop the excessive cross-posting to NAMD-l and VMD-l.
this is becoming *very* annoying.

pick one list and be done with it. if there is no response on that
list after, say, 2-3 days, try the other.

thanks in advance for your consideration,
      axel.

On Fri, May 4, 2018 at 12:04 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
>>>>
>>>
>>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.