Dear all,
do you have any additional info regarding this issue? I'm asking to decide
how to approach such simulations in alchemlyb.
*Domenico Marson*, Ph.D.
Ricercatore T.D. (A) | Research Fellow
Università degli Studi di Trieste | University of Trieste
Department of Engineering and Architecture (DEA)
Molecular Biology and Nanotechnology Laboratory @ UniTS (MolBNL.UniTs)
Via Valerio, 10 - 34127 Trieste (Italy)
domenico.marson.dia.units.it
+39 040 5583437
Skype: domenicomars
On Thu, Sep 29, 2022 at 8:02 PM Domenico Marson <domenico87.gmail.com>
wrote:
> Dear prof. Case,
> Thank you for taking this into consideration!
>
> I changed the lines you suggested, and indeed my problem is solved, as now
> DV/DL values are always printed!
>
> PS: I just removed the "if" blocks, leaving only the instruction to write
> si(si_dvdl),
> so now my pmend obviously writes always DV/DL values, even in simulations
> where TI calculations are not turned on.
> the
>
> if (si(si_dvdl) .ne. 0.d0)
> write(mdinfo, 9089) si(si_dvdl)
>
> could be replaced by
>
> if "ICFE flag is on"
> write(mdinfo, 9089) si(si_dvdl)
>
> (and similarly at lines 803-805) to avoid this problem, but I don't know
> anything about Fortran and the structure of pmemd code, so I followed the
> easter route for my test.
>
>
> *Domenico Marson*, Ph.D.
> Ricercatore T.D. (A) | Research Fellow
> Università degli Studi di Trieste | University of Trieste
> Department of Engineering and Architecture (DEA)
> Molecular Biology and Nanotechnology Laboratory @ UniTS (MolBNL.UniTs)
> Via Valerio, 10 - 34127 Trieste (Italy)
> domenico.marson.dia.units.it
> +39 040 5583437
> Skype: domenicomars
>
>
> On Thu, Sep 29, 2022 at 3:58 PM David A Case <david.case.rutgers.edu>
> wrote:
>
>> On Tue, Sep 27, 2022, Domenico Marson via AMBER wrote:
>>
>> >I had a conversation with Taisung, which I thank warmly for the detailed
>> >explanation of the situation.
>> >
>> >I have a further request "to whom it may concern": is it possible to have
>> >AMBER output DV/DL values even if they are exactly 0.0 when doing TI?
>>
>> I agree that this change would make sense; cc-ing to Taisung for his
>> consideration.
>>
>> If you want to explore, it looks (to my outsider's eye) like you could
>> just
>> change lines 803-805 and 986 in runfiles.F90 and recompile. Let us know
>> if
>> that allows your software to work better.
>>
>> ....dac
>>
>>
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Received on Sun Oct 16 2022 - 09:00:03 PDT
