Hi Saber:
thanks a lot for such kind reply.
How about the second question? I don't find any tutorial for the GBSA
solvent simulation in Gromacs website and I am not sure what kind of
parameters we should use for GBSA.
thank you very much
best
Albert
On 10/17/2012 05:48 PM, saber naderi wrote:
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 <[email protected]> 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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