[gmx-users] Structural features for LINCS application
Mark.Abraham at anu.edu.au
Fri Mar 16 01:38:00 CET 2012
On 16/03/2012 6:02 AM, Francesco Oteri wrote:
> Dear gromacs users,
> I am trying to simulate a protein (containing FeS cluster and a
> complex metal active site) using virtual site.
> I've to face a problem with LINCS. In particular, if I constrain only
> h-bonds without using virtual site,
> simulation runs fine but constraining "all-bonds", simulation crashes
> after a lot of LINCS warning like:
> Step 356, time 0.712 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.408533, max 8.159325 (between atoms 2750 and 2754)
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 2750 2754 90.0 0.1365 1.2502 0.1365
> In both cases simulation conditions are the same. The bonds causing
> problem belongs to the active site.
> I am wondering if there are structural features imparing the use of
> all-bonds constraints in LINCS.
> A second question is, how can I run MD with virtual site without
> all-bonds options.
Coupled constraints, such as you might have in a cluster, can be
delicate. Equilibrating with a quite small time step can be necessary.
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