[gmx-users] LINCS error with 3.3

[Yang Ye]

I have re-runed grompp with old topology.

David van der Spoel wrote:

>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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>>