Re: Setting integrator parameters for ABF

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Jul 27 2011 - 13:12:46 CDT

Hi Asjasja, that depends on which atoms you're applying the forces to. If
you apply them to hydrogens, these will move much faster than heavier atoms
for the same forces. Which atoms define the colvars that you're forcing
through ABF?

On Wed, Jul 27, 2011 at 1:49 PM, Ajasja Ljubetič
<ajasja.ljubetic_at_gmail.com>wrote:

> Dear all,
>
> To save computational time I would normally set the integration parameters
> to something like:
>
> timestep 2; #fs
> rigidBonds all
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 20
> longSplitting C2
> cutoff 12.
> switching on
> switchdist 10.
> pairlistdist 14
>
>
>
> Now I'm doing some ABF simulations in the membrane. Since
> ABF already infinitely helps with the sampling along my colvars, would it
> make sense to switch to more expensive but precise integrator parameters?
>
> timestep 1; #fs
> rigidBonds water
> nonbondedFreq 1
> fullElectFrequency 1
>
>
> I realize that all the degrees of freedom not in included the colvars are
> not better sampled (for example the lipid tails) so perhaps it's still
> better to go with the 2 fs time step...
> But on the other hand, the forces introduced by ABF might get quite large
> so a smaller timestep would insure a more stable simulation.
>
> Thank you for your advice and experience,
> Best regards,
> Ajasja Ljubetic,
> Young researcher
> Laboratory of biophysics
> Department F5
> Institute Jozef Stefan
> Ljubljana, Slovenia
>
>

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