[gmx-users] Problem with constraints in NVT calculations.

[Justin Lemkul]

On 9/29/14 8:01 AM, Kester Wong wrote:
> Dear all,
>
>
> I have been using the SWM4-NDP water model that works well with CHARMM27 force
> field.
>

Time out.  SWM4-NDP is a polarizable water model, and CHARMM27 is an additive 
force field.  The two are not compatible.  If you're using them together, you're 
basically just gambling that they work.  You shouldn't do this.

> The force field (most recent version) was obtained from virtualchemistry, and
> consists of polarisable ions and the SWM4-NDP water model from Lamoureux et al.
>
> The water on graphene (energy minimisation and NVT) calculations are stable, and
> have produced a few NVT runs of up to 10ns.
>
> I also compared the NVT runs with other previously calculated structures,
> namely, the visualised NVT runs are very much comparable to that obtained by
> CHARMM27 force field with TIPS3P water model.
>
>
> However, as the polarisable H3O+ and Cl- ions are inserted into the simulation
> box, the NVT run tends to crash as a result of too many LINCS warnings.
>
> I suspect that the constraints in the H3O is the cause of the LINCS warnings,
> and after removing the [ constraints ] in the topology file, the calculation
> seems to be running.
>
>
> ;[ constraints ]
>
> ;; i     funct   doh     dhh
>
> ;1 3      1       0.102
>
> ;1 4      1       0.102
>
> ;1 5      1       0.102
>
> ;3 4      1       0.169124
>
> ;4 5      1       0.169124
>
> ;3 5      1       0.169124
>
>
>
> Can anyone please tell me if what I am doing is correct?
>
> As I am not sure if removing the H3O constraints in the NVT run is appropriate.
>
>
> With regard to the massless Drude and standard oxygen mass (thank you Justin for
> providing the information), I would like to know why are they not appropriate
> (as mentioned in the previous email) for the SWM4-NDP model?
>

I wasn't making a declarative statement that it won't work.  I was asking 
whether anyone had verified that using a massless Drude in that model actually 
reproduced all of the physical properties of the SWM4-NDP model.  We do all of 
our development on the Drude FF with Drudes of mass = 0.4 amu and the extended 
Lagrangian.  I don't know how a massless Drude behaves in this model.  It may 
work fine, but you should very rigorously verify this yourself before doing 
anything by doing simulations of pure water.

-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

==================================================