[gmx-users] SETTLE and LINCS

[Justin Lemkul]

On 3/8/14, 6:08 PM, Andres Ortega wrote:
> Hi Dear Gromacs Users, i have read different post, of how to use settle for
> water and other constrain algorithm like shake or lincs for non-water bond,
> this can be use by adding
>
> -DFLEXIBLE,
>
> lincs
>
> non-water
>
> ?
>
>
> In old post, some of you said, that Flexible model should be use only for EM
> , and not for MD, so how is the correct way to use settle in MD simulations?
> or in the topol.top or water.itp put [constraints] ?
>

SETTLE is always invoked unless you use "define = -DFLEXIBLE," which you 
correctly note should not be done during MD.  The other constraint settings in 
the .mdp file relate to anything that's not water.  See the #ifdef statements in 
the .itp file for your chosen water model; it controls whether SETTLE is applied 
in the absence of -DFLEXIBLE.

-Justin

-- 
==================================================

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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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