[gmx-users] Converting TIPS3P model to SWM4-NDP model

[Justin Lemkul]

On 9/16/14 4:48 AM, Kester Wong wrote:
> Dear gromacs team,
>
>
> I have recently converted a TIPS3P system (10k molecules) to a SWM4-NDP model.
>
>
> As I followed the instruction as listed below, I find it hard for beginners like
> me to convert the water structure:
>
> http://www.gromacs.org/Documentation/How-tos/Changing_a_3_Point_Water_Model_to_a_4_Point_Water_Model
>
>
> Notwithstanding, after doing some reading and tinkering on the .gro file
> formatting, and tinkering, I have managed to convert TIPS3P water to SWM4-NDP
> models. I find this technique very useful, as I think I could probably save some
> computing time by having the first few ns of the equilibration of SWM4-NDP model
> done in a less expensive way (e.g. 3-point water model). It can be applied for
> other water models too, e.g. TIP3P to TIP4P and TIP5P conversions.
>

I don't know that there's much to gain by doing such conversions.  You still 
have to re-equilibrate no matter what, and the choice of TIP3P-equilibrated 
configuration is arbitrary; the final configuration of the simulation is not 
necessarily any better than any other snapshot, and you lose any semblance of 
continuity because you can't preserve the equilibrated ensemble of velocities, etc.

-Justin

>
> I have devised a short step-by-step note that I think might be useful to other
> gromacs users. This could also be a good opportunity to update the web page with
> more information?
>
>
> Please let me know if this is okay, and I will send the notes as a doc. attachment?
>
>
> Regards,
>
> Kester
>
>
>
>
>
>
>

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

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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