[9-VIII-2013]
Hi DAC and Thomas,
Thank you very much for your help (and I did not realise about the line 2778 in mdread.f).
Best regards.
Kepa K.
________________________________
De: "steinbrt.rci.rutgers.edu" <steinbrt.rci.rutgers.edu>
Para: AMBER Mailing List <amber.ambermd.org>
Enviado: Viernes 9 de agosto de 2013 16:46
Asunto: Re: [AMBER] TI with ifsc==2 (reposted)
Hi,
just an addition to what DAC said, there used to be the option to perturb
a system to nothing at all, i.e. disappear a complete simulation box with
everything in it. This was set by a special ifsc=2 option, because only
one prmtop was involved. The procedure turned out to be not useful for any
realistic simulation so it disappeared from the manual and should not be
used anymore.
The code may still technically allow it, but the 'ifsc==2' routines
could/should be removed just as well.
Kind Regards,
Thomas
On Fri, August 9, 2013 11:30 am, David A Case wrote:
> On Fri, Aug 09, 2013, Kepa K. Burusco wrote:
>>
>> if ( ifsc == 2)
>> ! If this is a perturb to nothing run, scale forces and calculate
>> dvdl
>> call sc_nomix_frc(f,nr3,ener)
>> ...
>> end if
>>
>> what does it mean "a perturb to nothing"?
>
> This is poor wording, historically left over from calling these procedures
> "double annihilation". The code is actually decoupling the chosen region
> from the rest of the system, i.e. removing all the force field terms that
> involve the interaction of the chosen region with its environment, but
> leaving
> intact those terms that involve atoms entirely within the chosen region.
> (cf. the discussion following Eq. 4.6).
>
> The ifsc=2 option is no longer supported (see line 2778 of mdread.F90).
> I'm
> not sure why references to it still appear elsewhere in the code, but
> suspect
> that reasons include an excess of caution or lack of time.
>
> ...dac
>
>
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>
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Fri Aug 09 2013 - 12:00:03 PDT
