[gmx-users] NVE Temperature Drift

[Justin Lemkul]

On 8/26/14, 9:29 AM, Johnny Lu wrote:
> I don't have much idea about the correct numbers to set. Mostly, I copy the
> old lysozyme tutorial (
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme_old/03_solvate.html),
> deleted the temperature and pressure couplings, and set the numbers bigger.
> I thought that bigger values won't make the simulation wrong, while smaller
> values might. Then, I ran it once, and found that the temperature seem to
> drop at 120,000 time step. So, in my second attempt, I only ran for 32,768
> time steps, changed the timestep, and then add the npt equilibration phase.
>
> Gromacs 4.6.6
>
> Water box 1.5 nm away from the protein:
> editconf -f $angle.complex.nowat.amber99sb.gro -o
> $angle.complex.nowat.amber99sb.newbox.gro -c -d 1.5 -bt dodecahedron
>
> While the old lysozyme tutorial (
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme_old/03_solvate.html)
> used a -d 1.0 waterbox, I worry that the NVE simulation would not be stable
> enough, so I put more water.
>
> I made up these three numbers:

If you use "made up" numbers, then expect made up results.  Cutoffs are part of 
the force field, you can't just change them and expect sensible behavior.

> rlist        = 1.8        ; short-range neighborlist cutoff (in nm)
> rcoulomb    = 1.5        ; short-range electrostatic cutoff (in nm)
> rvdw        = 1.5        ; short-range van der Waals cutoff (in nm)
>
> And set the cut offs larger than those in the tutorial, which used OPLS
> forcefield. What should be the correct numbers for Amber99SB? Where can I
> find those?
>

Try the primary literature reference for the force field.

-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

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