[gmx-developers] Simulated annealing problem

[Anton Feenstra]

Dear Guarav,

Please post user questions to the users list.

On 14/03/13 05:45, Gaurav Jerath wrote:
> Hi,
> I am trying to anneal two protein molecules.
> The usual protocol for a MD simulation was followed.
> But the problem arises that at high temperatures, the number of hydrogen
> bonds are increasing instead of getting decreased. The GROMOS43a1 force
> field was used and the mdp file for the simulation is shown below:
>
>
> ;
> title               =  Yo
> cpp                 =  /usr/bin/cpp
> constraints         =  all-bonds
> integrator          =  md
> dt                  =  0.002	;ps !
> nsteps              =  5000000	; total 10ns.
> ;nstcomm             =  1
> nstxout             =  250
> nstvout             =  1000
> nstfout             =  0
> nstlog              =  100
> nstenergy           =  100
> nstlist             =  10
> ns_type             =  grid
> rlist               =  1.0
> rcoulomb            =  1.0
> rvdw                =  1.0
> ; Berendsen temperature coupling is on in two groups
> 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        = 300  		300      ; reference temperature, one for each
> group, in K
> ; Energy monitoring
> energygrps          =  Protein  SOL
> ; Isotropic pressure coupling is now on
> Pcoupl              =  berendsen
> Pcoupltype          = isotropic
> tau_p               =  2.75
> compressibility     =  4.5e-5
> ref_p               =  1.0
> ; Generate velocites is off at 310 K.
> gen_vel             =  no
> gen_temp            =  300.0
> gen_seed            =  173529
> ; SIMULATED ANNEALING CONTROL =
> annealing               =  periodic periodic
> annealing_npoints        = 3 3
> annealing_time          = 0 5000 10000 0 5000 10000
> annealing_temp          = 300 500 300 300 500 300
>
>
> Kindly help me as I am unable to figure out if there is a problem in my
> parameters file
>


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | IBIVU/Bioinformatics - Vrije Universiteit Amsterdam   |
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|             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/         |
|             | "The Microsecond is Within Reach" (P.J. Van Maaren)   |
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