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

[Rakesh Ramachandran]

Hi Justin,

     Thanks for the reply. Sorry if this question was too long or I was not
clear.

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 ?

3) I was asking Berendsen pressure coupling with respect to the
equilibration stage, since I read in some earlier mailing post that
Berendsen coupling is more appropriate for temperature (NVT) as well as
pressure (NPT) equilibration.

4) Moreover once I do pbc correction I still see one or two ions sticking
out of the rhombic dodecahedron box representation in pymol. Is it more of
a visualization artifact ?

Regards
Rakesh

On 9 December 2015 at 21:04, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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