[gmx-users] LINCS error with 3.3

[Yang Ye]

Hi, David

The gmxcheck test result is that there is no difference between the two
tpr files.

Reading file md017_33.tpr, VERSION 3.3 (double precision)
Reading file md017_33b.tpr, VERSION 3.3_beta_20050202 (double precision)
Note: tpx file_version 37, software version 40
comparing inputrec
inputrec->sc_power (1 - 2)
comparing top
comparing idef
...

What you have said made me to test whether mdrun_3.3 could run tpr of
3.3b (version 37) (I am not using 3.2.1, but a CVS version). With
whatever tpr, mdrun_3.3 will crash the simulation after about 30 steps
(2fs per step). After the test, what I could conclude is that the
problem is *mdrun* itself. Any other information you need?

Yang Ye

David wrote:

>On Wed, 2005-10-12 at 23:20 +0800, Yang Ye wrote:
>  
>
>>I have re-runed grompp with old topology.
>>    
>>
>OK, please try this.
>
>run grompp with 3.2.1 and with 3.3 and then run gmxcheck -s1 321.tpr -s3
>330.tpr >& dump
>(you'll need gmxcheck from 3.3). Look for suspicious differences.
>
>Please do also run with the mdrun from 3.3 and the tpr file from 3.2.1
>
>Then please report back to the mailing list and/or open a bugzilla.
>
>Thanks for helping us debug gromacs 3.3.
>  
>
>>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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>>>>
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