[gmx-users] simulated annealing mdp

[Justin A. Lemkul]

On 6/12/12 3:39 AM, rama david wrote:
> Hi Gromacs Friends,
>
> I planed to do simulated annealing...
> My protocol is as follow
> ( forcefield G96 53a6   spc water model)
>
> 1. nvt at 310 k for 100 ps
> 2. Sa (mdp is posted below )
> 3. NPT at 310 k for 100 ps
>
> Is it right ??
>

There are two levels of "right" - suitability of purpose and syntactic 
correctness.  The latter is easily solved by running grompp.  If there's a 
problem, you'll know in five seconds rather than waiting a few hours for help. 
With respect to the former, you should decide on a protocol based on established 
procedures and the goals of your study.

There are many questions you should ask yourself.  What do you hope to achieve 
using the SA protocol shown?  How will it aid your study?  Should you use a 
wider range of temperatures for any particular reason?

 From what I see, you've got a protein in water and you're restraining the 
protein.  The SA protocol simply heats and cools water, which I don't think 
accomplishes much.

-Justin

> Please suggest me improvements...
>
> Sa mdp file
>
> title        = gromacs
> define        = -DPOSRES    ; position restrain the protein
>
> nstcomm        = 1
> comm-mode    = Linear; Run parameters
> integrator    = md        ; leap-frog integrator
> nsteps        = 500000        ; 2 * 50000 = 100 ps
> dt        = 0.002        ; 2 fs
> ; Output control
> nstxout        = 1000        ; save coordinates every 0.2 ps
> nstvout        = 1000        ; save velocities every 0.2 ps
> nstenergy    = 1000        ; save energies every 0.2 ps
> nstlog        = 1000        ; update log file every 0.2 ps
> ; Bond parameters
> continuation    = yes        ; Restarting after NVT
> 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)
> vdw-type        = Cut-off
> 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 is on
> tcoupl        = V-rescale    ; modified Berendsen thermostat
> tc-grps        = Protein Non-Protein    ; two coupling groups - more accurate
> tau_t        = 0.1    0.1    ; time constant, in ps
> ref_t        = 310     310    ; reference temperature, one for each group, in K
> ; Pressure coupling is on
> pcoupl        = Parrinello-Rahman    ; Pressure coupling on in NPT
> pcoupltype    = isotropic    ; uniform scaling of box vectors
> tau_p        = 2.0        ; time constant, in ps
> ref_p        = 1.0        ; reference pressure, in bar
> compressibility = 4.5e-5    ; isothermal compressibility of water, bar^-1
> ; Periodic boundary conditions
> pbc        = xyz        ; 3-D PBC
> ; Dispersion correction
> DispCorr    = EnerPres    ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel        = no        ; Velocity generation is off
> ; Simulated annealing
> annealing               = single single
> annealing_npoints        =  4  4
> annealing_time          =  0  200  400 600 0 200 400 600
> annealing_temp          = 310 323 300 310  310 323 300 310
>
>
>
>
> Thank you in advance
>
> With Best Wishes,
> Rama David
>
>

-- 
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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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