On Wed, Jan 26, 2022, Richard Kullmann wrote:
>
>I am doing regular MD simulations of 4 identical sugar chains. Each of
>these chains should have the C1-C2-C3-C4 dihedral angle in one of the
>sugars restrained. The contents of the restraints file are therefore:
>
> &rst iat = 3, 18, 16, 13,
> r1 = -58, r2 = -57, r3 = -37, r4 = -36,
> rk2 = 32.0, rk3 = 32.0, &end
> &rst iat = 201, 216, 214, 211,
> r1 = -58, r2 = -57, r3 = -37, r4 = -36,
> &end
> &rst iat = 399, 414, 412, 409,
> r1 = -58, r2 = -57, r3 = -37, r4 = -36,
> &end
> &rst iat = 597, 612, 610, 607,
> r1 = -58, r2 = -57, r3 = -37, r4 = -36,
> &end
>
>If now run these simulations and compare with simulations without
>restraints, I get a difference by a factor of 3. The input file is
>just standard in my opinion:
>
> nstlim=250000000,
Given that you think that a quarter of a billion steps is "standard", I'm
guessing that you are using pmemd.cuda.
I suspect that these restraints are being computed on the CPU. Experts
on cuda should chime in here.
....dac
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Received on Wed Jan 26 2022 - 12:30:02 PST
