[gmx-users] Fwd: Help with Gromacs 5.1 mdp options for CHARMM27 force field
Rakesh Ramachandran
korenpol3 at gmail.com
Wed Dec 9 04:44:12 CET 2015
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.
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.
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.
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.
Regards
Rakesh
On 6 December 2015 at 19:34, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 12/6/15 8:57 AM, Rakesh Ramachandran wrote:
>
>> Hi Justin,
>>
>> Thanks for the reply. Sorry if I am asking too many questions. I
>> wanted
>> to clarify some more doubts just to make sure I am performing the
>> simulation the right way.
>>
>> 1) What is the ideal Tcoupl option for CHARMM36 Nose-hoover or V-rescale.
>> Moreover I get the following note and warning when I use Nose-Hoover
>> thermostat.
>>
>>
> Use either; there is no force field dependence here.
>
> NOTE 1 [file npt.mdp]:
>> leapfrog does not yet support Nose-Hoover chains, nhchainlength reset
>> to 1
>>
>>
> Notes are for information only; they do not indicate a problem.
>
> WARNING 1 [file npt.mdp]:
>> For proper integration of the Nose-Hoover thermostat, tau-t (1) should
>> be
>> at least 20 times larger than nsttcouple*dt (0.08)
>>
>>
> Check your settings here. Warnings are important.
>
> So is V-rescale more optimal for Verlet cutoff and GPU based Gromacs.
>>
>> 2) Moreover I see in some publications that 0.9 nm to 1.0 nm for minimum
>> protein-edge distance is being used for Gromacs. Even in your tutorial you
>> mention using 1.0 nm. Taking into account minimum image convention should
>> it not be greater than 1.2 nm or is it highly dependent on the protein you
>> are simulating or rcouloumb cutoff or is dependent on Debye length.
>>
>>
> As long as the minimum image convention is not violated, there is no
> problem. Using a minimum solute-box distance equal to the longest cutoff is
> safe, but overkill. 1.0 nm is typically sufficient because then there are
> at least 2.0 nm between image atoms of, e.g. a protein, which is a couple
> of solvent shells and therefore enough.
>
> I would be grateful if you could clear my doubts on this aspect or point me
>> to the relevant literature. I am planning to use 1.25 nm for a salt conc
>> of
>> 300 mM MgCl2 with epsilon_r = 1 or should I use higher cutoff such as 1.4
>> nm. Moreover is the dielectric constant of the medium 82 for TIP3P water
>> model at 300K (ref http://www1.lsbu.ac.uk/water/water_models.html),
>>
>>
> Do not touch epsilon_r. Leave it at 1. It is not the dielectric
> constant; it is the reference for dielectric screening. If you change this
> value, you change in vacuo screening in a manner inconsistent with real
> physics and the force field parametrization.
>
> 3) In spite of running the NPT equilibration for 5 ns I am getting these
>> values and the RMSD values are also too high when the pressure parameter
>> is
>> measured. In your tutorial you had suggested to run longer NPT
>> equilibration if the density value does not converge to around 1000 kg/m^3
>> and pressure value around 1 bar. I found the same issue when I ran with
>> CHARMM27 force field and V-rescale thermostat. But on plotting I find the
>> results are similar to your plots in the tutorial but for 5 ns in both the
>> cases (CHARMM 27 and 36).
>>
>> for 1.25 nm protein-edge distance
>>
>> Pressure 1.52207 0.52 146.108 1.62992
>> (bar)
>> Density 1056.64 0.029 2.7515 -0.0336808
>> (kg/m^3)
>>
>> for 1.4 nm protein-edge distance
>>
>> Pressure 0.321022 0.94 137.028 2.4858
>> (bar)
>> Density 1054.45 0.053 2.67943 0.264365
>> (kg/m^3)
>>
>>
> Welcome to life when trying to simulate pressure.
>
> http://www.gromacs.org/Documentation/Terminology/Pressure
>
>
> -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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