[gmx-users] LINCS with amber99SB ?

Yun Shi yunshi09 at gmail.com
Tue Aug 9 17:37:43 CEST 2011

Hi all,

I want to do MD simulation with amber99SB force field, which I found
originally developed using SHAKE algorithm to constrain all bonds involving
hydrogen atoms. But it seems to me that SHAKE is still not supported with
domain decomposition in GROMACS4.5.4, and we can only use LINCS for bond
constraints if we want to run MD simulations in parallel.

So what should I use in simulating with amber99SB in parallel? LINCS
constraining allbonds? LINCS constraining hbonds only? Or just run with
SHAKE in one node?

I would be very grateful if someone could tell me the relative accuracy (or
if they are all good enough) and computational costs of these options above.

And maybe I should ask this question in the developers mailing list, but
would GROMACS support SHAKE in parallel in the near future, like in a 4.5.5

Thanks a lot,

Yun Shi
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