[gmx-users] some question about REMD

[saber naderi]

Hi Albert,

Regarding you first question, your protein is relatively big and in my
opinion 28 replicas is not much for a protein made of 290 AA with the
temperature range of 280-530. One thing that you can do is to use a lower
value for exchange probability to have less replicas. By doing this the
average time interval between exchanges becomes longer (assuming that you
keep the exchange attempt interval fixed). This is not necessarily a bad
thing because in case of large proteins the dynamics is slow anyway and it
is useful if you let the system relax between exchanges.

Cheers,
Saber

On 17 October 2012 17:32, Albert <mailmd2011 at gmail.com> wrote:

> hello:
>
>  I am going to perform replica exchange MD with Gromacs and I found some
> problems there:
>
> 1. my protein have around 290 aa with 4680 atoms. If I would like to
> perform with implicite solvent with exchange probability 0.2, I found from
> http://folding.bmc.uu.se/remd/ that I will have to generate around 28
> different replica between 280 and 530. However, I seldom see someone
> perform so much round of replicas......If I perform with explicit solvent
> with 8000 water molecules, the number of replica goes up to 112.... That'
> unbelievable a lot. My protein is a normal size and when we read the paper,
> usually people will produce no more than 12 replica. Why it is so much
> round for my case?
>
> 2. If I would like to perform in NVT with implicit solvent, shall I change
> something in the .mdp file? If the following (from Justine's tutorial) all
> right for the GBSA solvent?
>
> title       = Protein-ligand complex NVT equilibration
> define      = -DPOSRES  ; position restrain the protein and ligand
> ; Run parameters
> integrator  = md        ; leap-frog integrator
> nsteps      = 50000     ; 2 * 50000 = 100 ps
> dt          = 0.002     ; 2 fs
> ; Output control
> 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
> ; 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
> nstlist     = 5         ; 10 fs
> rlist       = 0.9       ; short-range neighborlist cutoff (in nm)
> rcoulomb    = 0.9       ; short-range electrostatic cutoff (in nm)
> rvdw        = 1.4       ; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype     = PME       ; Particle Mesh Ewald for long-range
> electrostatics
> pme_order       = 4         ; cubic interpolation
> fourierspacing  = 0.16      ; grid spacing for FFT
> ; Temperature coupling
> tcoupl      = V-rescale                     ; modified Berendsen thermostat
> tc-grps     = Protein_JZ4 Water_and_ions    ; two coupling groups - more
> accurate
> tau_t       = 0.1   0.1                     ; time constant, in ps
> 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         = xyz       ; 3-D PBC
> ; Dispersion correction
> DispCorr    = EnerPres  ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel     = yes       ; assign velocities from Maxwell distribution
> gen_temp    = 300       ; temperature for Maxwell distribution
> gen_seed    = -1        ; generate a random seed
>
>
> thank you very much
> best
> Albert
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