Hi,
That is what I expected, as I wrote in my previous mail.
You conformations are probably fine.
Berk
> Date: Mon, 16 Mar 2009 17:13:43 +0100
> From: andreas.fr...@ch.tum.de
> To: gmx-users@gromacs.org; oliver.dem...@ch.tum.de
> Subject: RE: [gmx-users] Wrong Shake Tolerance
>
Dear Berk,
thank you very much for the quick reply. We have used regular
reaction-field with cut-offs. The average temperature is not too low but
5K too high (compared with the adjustment of the temperature bath), but
it read on the user-list that this behavior is common when using RF. We
are
; From: andreas.fr...@ch.tum.de
> To: gmx-users@gromacs.org; oliver.dem...@ch.tum.de
> CC:
> Subject: [gmx-users] Wrong Shake Tolerance
>
> Dear Gromacs-Users,
>
> we have the following problem: after running several hundred nanoseconds
> of a peptide (Gromos FF 53a6) in spc-water
Dear Gromacs-Users,
we have the following problem: after running several hundred nanoseconds
of a peptide (Gromos FF 53a6) in spc-water (NpT ensemble), we recognized
that the tolerance of shake (all-bonds were constrained) was wrongly
adjusted: instead of calculating with shake_tol = 0.0001, t
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