[gmx-users] LINCS error with 3.3

[David van der Spoel]

On Wed, 2005-10-12 at 18:11 +0800, Yang Ye wrote:
> Hi, Eric
> 
> We tried to use release-3.3 to continue the running our existing 
> simulations, on two platforms (x86_64 and alpha), with two systems (one 
> big and one small ~20000 atoms). But we got lots of LINCS warning for 
> both of them within 30 steps of the simulation, e.g.
> 
> Step 22, time 0.044 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max inf (between atoms 74 and 75) rms inf
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>      71     72   90.0    0.1090   0.8407      0.1090
>      74     75   90.0    0.1090 
> 311257572943502531345973775419542153121393363270638764032.0000      0.1090
>      93     94   90.0    0.1090      inf      0.1090
>      93     95   90.0    0.1090      inf      0.1090
> 
> release-3.3 also generate lots of LINCS warnings with newly started system.
> 
> Please advice whether you need more information to diagnose this?
Yes we need quite a bit more information. Did you rerun grompp with old
topologies, did you use an old tpr file, or did you make a new tpr with
tpbconv, if so which version?




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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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