[1-X-2012]
Hi all,
Thank you very much for your help Dr. Case, but I am still confused: your suggestion is precisely what I did the first time when I got he error message (at least, I think so). In my input file I selected ntc=2, ntf=2, and then I applied the noshakemask to turn off shake in the solute (GLA in state V0 and GLB in state V1).
I send the output files (with the input and the error message) attached to this email in case that it can help.
Thanks for your help.
Kepa K.
******************************************************************
________________________________
De: David A Case <case.biomaps.rutgers.edu>
Para: Kepa K. Burusco <kekoburgo.yahoo.es>; AMBER Mailing List <amber.ambermd.org>
Enviado: Lunes 1 de octubre de 2012 2:49
Asunto: Re: [AMBER] TI Softcore potentials and SHAKE
On Mon, Oct 01, 2012, Kepa K. Burusco wrote:
>
> So, just to be sure that I understood you correctly: if I run a TI
> simulation asking for jfastw=0 (by default), ntc=1 and ntf=1, do you
> mean that "sander" automatically recognises TIP3P water molecules as
> RIGID ones by default and does the calculation SHAKEing the solvent but
> not the solute? Because this is the case I am interested in.
No, this is not correct. If you want to avoid shake in part or all of the
solute, turn SHAKE on (with ntc=2), but use the noshakemask string to turn off
shake for any parts of the solute where the atom types are changing between V0
and V1.
....dac
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Received on Mon Oct 01 2012 - 03:30:03 PDT
