[gmx-users] some question about REMD

[Justin Lemkul]

On 10/17/12 1:52 PM, Albert wrote:
> Hi Justin:
>
> Thank you very much for eply.
>
> So the modified .mdp file (including the GBSA model setting) is the following?
> Is this correct?
>

No.  See inline comments.

> title = Protein-ligand complex NVT equilibration
> define = -DPOSRES ; position restrain the protein and ligand

There is no need for restraints.  There is no solvent to equilibrate around the 
protein.

> ; Run parameters
> integrator = sd ;
> nsteps = 50000 ; 2 * 50000 = 100 ps
> dt = 0.002 ; 2 fs
> nstxout = 100 ; save coordinates every 0.2 ps
> nstvout = 100 ; save velocities every 0.2 ps
> nstenergy = 100 ; save energies every 0.2 ps
> nstlog = 100 ; update log file every 0.2 ps
> energygrps = Protein JZ4

This is only appropriate if you're following the tutorial exactly.  From your 
previous description, you are dealing with a protein and no ligand.

> ; Bond parameters
> continuation = no ; first dynamics run
> constraint_algorithm = lincs ; holonomic constraints
> constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained
> lincs_iter = 1 ; accuracy of LINCS
> lincs_order = 4 ; also related to accuracy
> ; Neighborsearching
> ns_type = grid ; search neighboring grid cells

You need ns-type = simple.

> nstlist = 5 ; 10 fs

Set nstlist = 0 for a fixed neighbor list.  In conjunction with infinite 
cutoffs, you will use the all-vs-all kernels, which are highly optimized.

> rlist = 0 ; short-range neighborlist cutoff (in nm)
> rcoulomb = 0 ; short-range electrostatic cutoff (in nm)
> rvdw = 0 ; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics

Set coulombtype = cutoff.

> pme_order = 4 ; cubic interpolation
> fourierspacing = 0.16 ; grid spacing for FFT
> ; Temperature coupling
> tcoupl = V-rescale ; modified Berendsen thermostat

Note that tcoupl is ignored when using the sd integrator.

> tc-grps = Protein_JZ4 Water_and_ions ; two coupling groups - more accurate

You don't have water and ions in an implicit system, and likely you don't have a 
ligand.

> tau_t = 0.1 0.1 ; time constant, in ps

tau_t is too low for sd, use something like 1.0.

> ref_t = 300 300 ; reference temperature, one for each group, in K
> ; Pressure coupling
> pcoupl = no ; no pressure coupling in NVT
> ; Periodic boundary conditions
> pbc=no
> ; Dispersion correction
> DispCorr = EnerPres ; account for cut-off vdW scheme

Unnecessary with infinite cutoffs.

> ; Velocity generation
> gen_vel = yes ; assign velocities from Maxwell distribution
> gen_temp = 300 ; temperature for Maxwell distribution
> gen_seed = -1 ; generate a random seed
>
> ; IMPLICIT SOLVENT ALGORITHM
> implicit_solvent = yes
>
> ; GENERALIZED BORN ELECTROSTATICS
> ; Algorithm for calculating Born radii
> gb_algorithm = OBC
> ; Frequency of calculating the Born radii inside rlist
> nstgbradii = 1

This should also be set to zero.

> ; Cutoff for Born radii calculation; the contribution from atoms
> ; between rlist and rgbradii is updated every nstlist steps
> rgbradii = 5

Set to zero.

-Justin

> ; Dielectric coefficient of the implicit solvent
> gb_epsilon_solvent = 80
> ; Salt concentration in M for Generalized Born models
> gb_saltconc = 0
> ; Scaling factors used in the OBC GB model. Default values are OBC(II)
> gb_obc_alpha = 1
> gb_obc_beta = 0.8
> gb_obc_gamma = 4.85
> gb_dielectric_offset = 0.009
> sa_algorithm = Ace-approximation
> ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
> ; The value -1 will set default value for Still/HCT/OBC GB-models.
> sa_surface_tension = -1
>
>
>
> On 10/17/2012 07:45 PM, Justin Lemkul wrote:
>>
>>
>> On 10/17/12 1:43 PM, Albert wrote:
>>> hello Justin:
>>>
>>> thanks a lot for kind reply.
>>> I've got another question: how to disable PBC? shall I simply delete "pbc=xyz"
>>> from .mdp file? I found that sometimes if we delete some parameters from .mdp,
>>> gromacs will use the default instead of disable it.
>>>
>>
>> The default setting for pbc is xyz, so deleting the line accomplishes nothing.
>> Set "pbc = no" in the .mdp file.
>>
>> -Justin
>

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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