[gmx-users] Heating error

[Justin A. Lemkul]

mohammad reaza dayer wrote:
> 
> 
> Dear Justin
> Greetings:
> 
> I want to melt up hemoglobin, using simulated annealing methods. I used 
> the following mdp file parameters:
> ****************************************************
> constraints    =    all-bonds
> integrator    =    md
> dt    =    0.002 ; ps !
> nsteps    =    100000 ; total 100.0 ps.
> tinit    =    0
> init_step    =    0
> nstcomm    =    1
> nstxout    =    500 ; collect data every 0.5 ps
> nstvout    =    1000
> nstfout    =    100
> nstlog    =    10
> nstenergy    =    100
> nstlist    =    100
> ns_type    =    grid
> pbc    =    xyz
> rlist    =    1.0
> coulombtype    =    PME
> rcoulomb    =    1.0
> vdwtype    =    cut-off
> rvdw    =    1.4
> fourierspacing    =    0.08
> fourier_nx    =    0
> fourier_ny    =    0
> fourier_nz    =    0
> pme_order    =    8
> ewald_rtol    =    1e-5
> optimize_fft    =    yes
> nstcomm    =    1
> comm-grps    =    Protein    Non-Protein
> Tcoupl    =    no
> tau-t    =    0    0
> tc-grps    =    Protein    Non-Protein
> ref-t    =    310    310
> solvent_optimization    =    sol
> energygrps    =    Protein    Non-Protein
> Pcoupl    =    berendsen
> Pcoupltype    =    isotropic
> tau_p    =    0.5
> compressibility    =    4.5e-5
> ref_p    =    1.0
> gen_vel    =    no
> gen_temp    =    310
> gen_seed    =    173529
> annealing    =    yes    yes
> annealing    =    single    single
> annealing_npoints    =    100    100
> annealing_time    =    0    1    2    3    4    5    6    7    8    9    
> 10    11    12    13    14    15    16    17    18    19    20    21    
> 22    23    24    25    26    27    28    29    30    31    32    33    
> 34    35    36    37    38    39    40    41    42    43    44    45    
> 46    47    48    49    50    51    52    53    54    55    56    57    
> 58    59    60    61    62    63    64    65    66    67    68    69    
> 70    71    72    73    74    75    76    77    78    79    80    81    
> 82    83    84    85    86    87    88    89    90    91    92    93    
> 94    95    96    97    98    99    0    1    2    3    4    5    6    
> 7    8    9    10    11    12    13    14    15    16    17    18    
> 19    20    21    22    23    24    25    26    27    28    29    30    
> 31    32    33    34    35    36    37    38    39    40    41    42    
> 43    44    45    46    47    48    49    50    51    52    53    54    
> 55    56    57    58    59    60    61    62    63    64    65    66    
> 67    68    69    70    71    72    73    74    75    76    77    78    
> 79    80    81    82    83    84    85    86    87    88    89    90    
> 91    92    93    94    95    96    97    98    99
> annealing_temp    =    310    311    312    313    314    315    316    
> 317    318    319    320    321    322    323    324    325    326    
> 327    328    329    330    331    332    333    334    335    336    
> 337    338    339    340    341    342    343    344    345    346    
> 347    348    349    350    351    352    353    354    355    356    
> 357    358    359    360    361    362    363    364    365    366    
> 367    368    369    370    371    372    373    374    375    376    
> 377    378    379    380    381    382    383    384    385    386    
> 387    388    389    390    391    392    393    394    395    396    
> 397    398    399    400    401    402    403    404    405    406    
> 407    408    409    310    311    312    313    314    315    316    
> 317    318    319    320    321    322    323    324    325    326    
> 327    328    329    330    331    332    333    334    335    336    
> 337    338    339    340    341    342    343    344    345    346    
> 347    348    349    350    351    352    353    354    355    356    
> 357    358    359    360    361    362    363    364    365    366    
> 367    368    369    370    371    372    373    374    375    376    
> 377    378    379    380    381    382    383    384    385    386    
> 387    388    389    390    391    392    393    394    395    396    
> 397    398    399    400    401    402    403    404    405    406    
> 407    408    409    310
> ****************************************************************
> the simulation started with no warning but unfortunately the protein 
> temperature increased for up to
> 2-3 ps and after that decreased to low temperatures. I have studies most 
> of e-mails in gmx-archives regarding such error and tried all of them 
> but I could not solve the problem. I will appreciate if your kindly help me.

It is useful to actually provide the link for any pertinent post for reference.

I think you're making the problem too complicated.  Simulated annealing 
increases the temperature linearly (per the  manual), so I really see no need to 
specify each time point individually, although I don't know why it doesn't work. 
  Simplify the problem:

annealing    =    yes    yes
annealing    =    single    single
annealing_npoints    =    2    2
annealing_time	     =    0    100    0    100
annealing_temp	     =    310  409    310  409

In theory, the above should give you steadily-rising temperature over 100 ps.

-Justin

> Best Regards
> dayer 
> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================