[gmx-users] CHARMM Pulling LINCS Error

[Justin Lemkul]

On 6/18/15 1:40 PM, Todd 53148 wrote:
> Dear Gromacs Users,
>
> I have been trying to pull my protein's center of mass away from the
> alpha-carbon of a residue.  My pull group consists of non-hydrogens at
> least 3 residues distant from the tether residue, which is restrained.
>
> I am using implicit solvent in gromacs 4.5.5, pulling at 0.000005nm/ps with
> a 0.002 dt.  I have equilibrated for 100ns, and I do not think that more
> equilibration is necessary.  Equilibration generated no LINCS errors.
>
> With pulling and restraint force constants of 3000kJ/(mol*nm^2), I
> generated LINCS errors at about step 30 of the pull.  They were also
> generated at a pulling rate of 0.  I was able to do the same experiment in
> OPLS-AA with no LINCS errors.
>
> I decreased the force constants to 1000, and only got a LINCS error for one
> of 50 pulls (50 different residues' CAs).
>

1 out of 50 failing simply suggests the stochastic nature of the process. 
Probably whatever the initial conditions were, combined with the pull vector, 
caused random instability.  With the stiff force constant above, you're probably 
just increasing the likelihood of really nasty forces abusing the protein.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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