[gmx-users] some question about REMD
saber naderi
sbrnaderi at gmail.com
Wed Oct 17 18:18:05 CEST 2012
I am no expert in implicit solvent simulations but I think for these
simulations it is better to use stochastic dynamic integrators with no
pbc (instead of NVT) and infinite (or very large) cut-off distances because
there is no actual water molecule in your simulation box and [normally] you
do not have to worry about the boundary effects.
For finding appropriate parameters, you should have a look at the Gromacs
manual and read the literature but if you need a quick example see below
(please note that this is just an example).
Cheers,
Saber
; RUN CONTROL PARAMETERS
integrator = sd
tinit = 0 ; Starting time
dt = 0.002 ; 2 femtosecond time step for integration
nsteps = 50000
; OUTPUT CONTROL OPTIONS
nstxout = 50000 ; Writing full precision coordinates every
nanosecond
nstvout = 50000 ; Writing velocities every nanosecond
nstfout = 0 ; Not writing forces
nstlog = 2500 ; Writing to the log file every step
nstenergy = 2500 ; Writing out energy information every step
nstxtcout = 2500 ; Writing coordinates every 5 ps
energygrps = System
; NEIGHBORSEARCHING PARAMETERS
nstlist = 0
ns-type = simple
pbc = no
rlist = 0
; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype = cut-off
rvdw = 0
rcoulomb = 0
; Temperature coupling
tc-grps = System
tau_t = 10
ref_t = 300
ld_seed = 123
;implicit solvent
implicit_solvent = GBSA
gb_algorithm = OBC
rgbradii = 0
gb_epsilon_solvent = 80
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = yes
gen_temp = 300
comm_mode = Angular
; OPTIONS FOR BONDS
constraints = all-bonds
constraint-algorithm = Lincs
unconstrained-start = yes
lincs-order = 4
lincs-iter = 1
lincs-warnangle = 30
On 17 October 2012 17:51, Albert <mailmd2011 at gmail.com> wrote:
> 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 <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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