[gmx-users] some question about REMD

[Albert]

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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