[gmx-users] distance restraints and lincs warning
Kai Zhuang
kai.zhuang at gmail.com
Tue Jun 21 21:10:42 CEST 2005
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
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