[gmx-users] LINCS error with 3.3
leafyoung81-group at yahoo.com
Wed Oct 12 17:20:29 CEST 2005
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:
>>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
>> 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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