[gmx-users] LINCS vs SHAKE!

Mark Abraham mark.j.abraham at gmail.com
Sun Oct 21 13:49:58 CEST 2012

Please choose a relevant subject line!
On Oct 21, 2012 10:37 PM, "Arman M. Soufiani" <armansoufiani at gmail.com>
> Dear Gromacs users,
> I want to run an NVT md. I am using LINCS algorithm to constrain both a
> polymer and protein in my solvated system.
> Some of my dihedral types are tabulated functions. I am running the
> equilibration on one node and there is no domain decomposition.
> All together, when I run the NVT my system explodes and I receive the
> following warning and errors:
>  *WARNING: For the 15 non-zero entries for table 0 in table_d1.xvg the

You're approximating a potential function over a full rotation with a
stepwise approximation of only 15 points? Either get more, or fix the file
format if you should have had more.

> forces deviate on average 281% from minus the numerical derivative of the
> potential*
> *relative constraint deviation after LINCS:
> rms 2.431943, max 26.861526 (between atoms 713 and 714)
> bonds that rotated more than 30 degrees:*
> I really have no idea what should I do?

Demonstrate your system is fine with normal dihedrals.


> I am opt for providing more information of the system I am working with.
> Thank you in advance,
> BR
> Arman
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