[gmx-users] Fwd: Help with Gromacs 5.1 mdp options for CHARMM27 force field

[Justin Lemkul]

On 12/8/15 10:43 PM, Rakesh Ramachandran wrote:
> Hi Justin,
>
>     Thanks for the reply. I have few more doubts regarding the mdp settings
> and gmx tools related analysis.
>
> 1) What are the optimal values of tau_t and tau_p for CHARMM36. I see in
> your tutorial that it is 0.1 0.1 for tau_t and 2.0 for tau_p. The
> CHARMM-GUI generated mdp settings had 1.0 1.0 for tau_t and 5.0 for tau_p.
> So are higher values more appropriate for CHARMM36 FF and what properties
> does it effect ? Moreover during NPT equilibration is Berendsen pressure
> coupling necessary or can I use Parinello-Rahman directly.
>

Never use Berendsen pressure coupling during production data collection. Its 
ensemble is not a true NPT ensemble. These settings are not dependent on force 
field.

> 2) My protein has MG bound so is CHARMM36 FF enough or some kind of
> parameterization needs to be performed before running MD. Moreover what
> precautions or steps should I take before running MD in this case. The
> crystal structure is at pH 7.5 so is the protonation determined by pdb2gmx
> enough.
>

No additive force field treats divalent ions particularly well.

Do pKa calculations and set ionization states accordingly.

> 3) I want to keep crystallographic waters (lining the protein surface as
> well as the binding site) but I find that the box size increases too much
> even when I use minimum solute-box distance of 1.0 nm. So my question is
> can I use a fixed box size of 10nm for rhombic dodecahedron, since I know
> that without the crystallographic waters with (-d 1.4 nm) the size would be
> 100^3A3. Will it lead to violating the minimum image convention or is there
> a way in gromacs which can account for the crystallographic waters.
>

Crystal waters should not have a significant impact on box dimensions. Usually 
no more than one solvation shell is present.  Decide the box size based on the 
solute; not waters attached to it.  Once you start dynamics, differentiating 
between crystal and bulk waters becomes largely irrelevant for anything at the 
surface.

> 4) I was also confused with respect to the periodicity effects removal, So
> using trjconv is this order correct -pbc whole -> -pbc nojump -> -pbc mol
> -center -ur compact (for System). Moreover what is the preferred reference
> for analysis the md.tpr (production run input file) or the crystal
> structure.
>

The reference can be whatever you like.

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow

-Justin

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

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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