[gmx-users] distance restraints and lincs warning

[Kai Zhuang]

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
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-- 
Kai Zhuang
BioMedical Engineering @ University of Toronto
kai dot zhuang at gmail dot com
kai.zhuang at gmail.com
6478314789