Re: [AMBER] TI Softcore potentials and SHAKE

From: Kepa K. Burusco <kekoburgo.yahoo.es>
Date: Mon, 1 Oct 2012 11:17:52 +0100 (BST)

[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
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