[gmx-users] Structural features for LINCS application

[Mark Abraham]

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.

Mark