[gmx-users] correct rlist and Verlet scheme

Timofey Tyugashev tyugashev at niboch.nsc.ru
Fri Feb 19 12:31:48 CET 2016

Yes, the implementation is clearly different from AMBER and I don't 
really want to try hard to get Identical results.
I picked AMBER ff99sb-ildn because it looked to be both quite popular 
for protein and nucleic acids simulations (going by the number of cites 
for its paper)  and reasonably recent.
Our home-grown software uses a derivative of ff99 for implicit solvent 
calculations, so I wanted to spare myself the trouble of parametrising 
non-standard residues and ligands by using a ff from the same family and 
using already existing ones.

So i'm interested  in simply running it in gromacs with adequate setup. 
And I'm just not sure what .mdp parameters to set.

For P.S.: Different version of it. Authors use different cutoffs.

17.02.2016 23:16, gromacs.org_gmx-users-request at maillist.sys.kth.se пишет:
> Message: 1
> Date: Wed, 17 Feb 2016 18:07:28 +0100
> From: Szil?rd P?ll<pall.szilard at gmail.com>
> To: Discussion list for GROMACS users<gmx-users at gromacs.org>
> Cc: Discussion list for GROMACS users
> 	<gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] correct rlist and Verlet scheme
> Message-ID:
> 	<CANnYEw6z_zvQajdtYiPLSqr6J1Cb7=3uX93LT9GS6U6HkVK8Xw at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
> Hi,
> The short-range interaction treatment in AMBER and GROMACS is quite
> different (to the best of my knowledge), so obsessing about rlist
> seems pointless to me.
> AMBER uses a heuristic list update where search is triggered based
> particles tracking ("safe" but inefficient strategy), whereas GROMACS
> uses a fixed list update frequency. The automated buffer estimate that
> ensures control of the non-boneded drift. Without controlling_both_
> buffer and search frequency (and a bunch of other subtle
> implementation details) you won't achieve identical computation.
> Hence, if you want to have (more or less) the same non-bonded
> calculation implemented in GROMACS, strictly speaking you'd have to
> use nstlist=1 or if you accept to be a bit less strict, a huge manual
> buffer (and small-ish nstlist) should achieve more or less the same.
> However, there are plenty of other algorithmic and implementation
> differences between AMBER and GROMACS, so I don't think it's worth
> worrying about getting the Verlet list buffer length to match.
> Cheers,
> --
> Szil?rd
> PS: I thought AMBER FF was parametrized with 0.9 nm cut-off, isn't it?

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