[gmx-users] distance restraints and lincs warning

[T.A.Wassenaar]

Hi Kay,

The error is the general LINCS-can't-manage error, which 
can have numerous causes. If this happens early in the 
simulation (during position restraint run), there is 
probably something wrong with your system, e.g. with the 
topology. Did you get any warnings when running grompp?

In Aldo's case, it's unclear why it happens, especially 
since it doesn't happen when using version 3.1.4 It may be 
a bug in the handling of the distance restraints, but I 
haven't tried that in >3.2 versions myself. Maybe one of 
the developpers can comment on the possibility.

Hope it helps,

Tsjerk

On Tue, 21 Jun 2005 15:10:42 -0400
  Kai Zhuang <kai.zhuang at gmail.com> wrote:
> i have an very similar situation:
> running position restrained simulation on a dimeric 
>protein:
> very simular erros, runs for 8 steps, producing a 
>similar error each
> step, then dies.
> 
> help?
> 
> On 6/20/05, A.Rampioni <A.Rampioni at rug.nl> wrote:
>> Dear colleagues,
>> 
>> I am performing some simulations on the following 
>>system:
>> 3 peptide in a beta-sheet configuration + other 3 
>>peptides
>> in a beta-sheet configuration 1 nm far apart in a
>> truncated octahedron box.
>> I imposed on both the trimers improper dihedral 
>>restraints
>> on one peptide and distance restraints among the 
>>peptides
>> of the trimer.
>> I want to bring the two trimers close together, so I
>> imposed some distance restraints even between the 
>>trimers.
>> 
>> I have performed an energy minimization of the starting
>> configuration and a further mdrun with position 
>>restraints
>> (without distance restraints) for  10 ps.
>> 
>> Then I turn on distance restraints and WITH THE VERSION
>> 3.1.4 EVERYTHING WORKS, BUT WITH THE VERSION 3.2.1 IT 
>>DOES
>> NOT WORK !!!
>> 
>> Here I give you the distance restraints that I have 
>>used.
>> When I use the first 8 dist.res. and just one of the 
>>last
>> four (it doesn't matter which one, but just one!) it 
>>works
>> for both the versions, otherwise only version 3.1.4 
>>works.
>> 
>> [ distance_restraints ]
>> ;  ai    aj    type    index    type    low    up1 
>>   up2
>>    fac
>>     25   137     1        0       1      0.0    0.6 
>>   0.8
>>    0.2
>>     73   185     1        1       1      0.0    0.6 
>>   0.8
>>    0.2
>>    137   249     1        0       1      0.0    0.6 
>>   0.8
>>    0.2
>>    185   297     1        1       1      0.0    0.6 
>>   0.8
>>    0.2
>>    361   473     1        0       1      0.0    0.6 
>>   0.8
>>    0.2
>>    409   521     1        1       1      0.0    0.6 
>>   0.8
>>    0.2
>>    473   585     1        0       1      0.0    0.6 
>>   0.8
>>    0.2
>>    521   633     1        1       1      0.0    0.6 
>>   0.8
>>    0.2
>>     25   424     1        2       1      0.0    0.6 
>>   0.8
>>    0.2
>>     73   379     1        3       1      0.0    0.6 
>>   0.8
>>    0.2
>>    249   648     1        2       1      0.0    0.6 
>>   0.8
>>    0.2
>>    297   603     1        3       1      0.0    0.6 
>>   0.8
>>    0.2
>> 
>> Here I list the options about dist. res. that I have 
>>used
>> 
>> disre                    = simple
>> disre_weighting          = equal
>> disre_mixed              = no
>> disre_fc                 = 1000
>> disre_tau                = 0
>> nstdisreout              = 100
>> 
>> 
>> Here it is the MESSAGE ERROR:
>> 
>> Step 0, time 0 (ps)  LINCS WARNING
>> relative constraint deviation after LINCS:
>> max 183.362411 (between atoms 444 and 445) rms 23.975990
>> bonds that rotated more than 30 degrees:
>>   atom 1 atom 2  angle  previous, current, constraint
>> length
>>      415    416  110.7    0.1471   0.1564      0.1470
>>      416    417  114.1    0.1526   0.1499      0.1530
>>      416    420   49.9    0.1530   0.5337      0.1530
>>      417    418   35.6    0.1531   0.1890      0.1530
>>      420    422  109.8    0.1327   5.3983      0.1330
>>      422    424  178.6   10.1607  12.4716      0.1470
>>      424    425  175.0   10.2412  12.6243      0.1530
>>      424    438  178.1   10.3766  13.3002      0.1530
>> 
>> 
>> 
>> Any idea of what can be wrong?
>> 
>> Thanks
>> 
>> Aldo
>> _______________________________________________
>> gmx-users mailing list
>> gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please don't post (un)subscribe requests to the list. 
>>Use the
>> www interface or send it to 
>>gmx-users-request at gromacs.org.
>> 
> 
> 
> -- 
> Kai Zhuang
> BioMedical Engineering @ University of Toronto
> kai dot zhuang at gmail dot com
> kai.zhuang at gmail.com
> 6478314789
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. 
>Use the 
> www interface or send it to 
>gmx-users-request at gromacs.org.