Hi Kepa,
I am not sure, but my interpretation of this sentence:
"Note that a different setup is required, so prmtop files for non soft
core simulations cannot be used with soft core potentials and vice versa".
is this:
A)
You may use TI (connected with "appearing/disappearing" atoms) without
soft core potentials
then your prmtop files (for state 0 and 1) have to have the same number of
atoms so the atoms which are not present in one of the state (0 or 1) have
to be still present in both prmtop files but in one prmtop file just as a
dummy atoms (the rest atoms are identical in both systems).
B)
On the other hand if you use soft core potentials for this task, both
prmtop files differ
in number of atoms as you do not use dummy atoms here for "disappeared"
atoms but
you simply omit them in the given prmtop file while maintaining the rest
of the atoms identical in both prmtop files.
The above sentence is perhaps telling you that you cannot use prmtop files
prepared in case A)
for soft core TI and vice versa.
So this is my interpretation and if it is wrong Thomas Steinbrecher will
for sure
correct me soon :))
Best,
Marek
Dne Mon, 16 Jul 2012 20:30:24 +0200 Kepa K. Burusco <kekoburgo.yahoo.es>
napsal/-a:
> [16-VII-2012]
>
> Hi Everybody,
>
> I would like to run some tests for a Free Energy Calculation using
> Termodynamic Integration (TI) and softcore potentials in sander
> (amber11).
>
>
> I have prepared my input files (coordinates and topology) for states 0
> and 1 with LEaP following the information given in Tutorial A9 (in amber
> tutorials webpage). I have also been reading the Amber11 manual about TI
> and sander. Then, when reading the different flags/options for "ifsc" it
> says that you have to select ifsc=1 to activate the softcore potentials
> BUT it also continues with:
>
> "Note that a different setup is required, so prmtop files for non soft
> core simulations cannot be used with soft core potentials and vice
> versa".
>
> I have been reading also LEaP info at AmberTools11 manual but I have not
> found any remark about this...
>
> I thought that the parmtop files for MD calculations were basically
> compatible with TI calculations. Can anyone tell me what are the
> differences between the parmtop files for non-SC potentials / SC
> potential simulations? Then, how should I proceed to create the parmtop
> files with LEaP for TI and SC potentials?
>
> Thank you very much.
>
> Kepa K.
>
>
> **********************************
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> __________ Informace od ESET NOD32 Antivirus, verze databaze 7303
> (20120716) __________
>
> Tuto zpravu proveril ESET NOD32 Antivirus.
>
> http://www.eset.cz
>
>
>
--
Tato zpráva byla vytvořena převratným poštovním klientem Opery:
http://www.opera.com/mail/
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jul 16 2012 - 12:30:02 PDT
