Antw: [gmx-users] Problem with simulated annealing!!!

[Peter Friedel]

dear poornima,

I saw the parameterfile and could see that the word

"annel" (your choice) is not the right
"anneal"

can you see it too ...?
sincerely, peter

Dr. Peter Friedel
Hohe Str. 6, 01069 Dresden
Institut für Polymerforschung Dresden e.V.
Tel.: 0351-4658289
Fax: 0351-4658565
email: friedel at ipfdd.de
>>> poornings at yahoo.co.in 29.03.06 13.02 >>>
Dear GMX users,

We are using GROMACS version 3.2.1. I am trying to do
simulated annealing. But when I use the following 
parameters and do the MD, it is working with the
reference temperature and not with which is given in
the parameter file.. 

And I tried with the example parameters which is given
in the manual(version 3.2). For that MD also the job
running with the reference temperature and not with
the parameters from the *.mdp file. In both MD runs
the temperature starts with 0K and drastically
increases to 300 K and stays there as shown below.

this is my md.mdp file 


;	Input file
;
title               =   Simulated annealing 
cpp                 =  /lib/cpp
constraints         =  all-bonds
integrator          =  md
dt                  =  0.002	; ps !
nsteps              =  5000	; total 10 ps.
nstcomm             =  1
nstxout             =  50
nstvout             =  10
nstfout             =  0
nstlog              =  10
nstenergy           =  10
nstlist             =  10
ns_type             =  grid
rlist               =  1.0
rcoulomb            =  1.0
rvdw                =  1.0
; Berendsen temperature coupling is on in two groups
Tcoupl              =  berendsen
tc-grps		    =  Protein	SOL
tau_t               =  0.1	0.1
ref_t               =  300	300
; Energy monitoring
energygrps          =  Protein  SOL
; Isotropic pressure coupling is now on
Pcoupl              =  berendsen
Pcoupltype          = isotropic
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0
;simulated annealing
anneling            =  single
anneling_npoints    =  5 
anneling_time       =  2 4 6 8 10
anneling_temp       =  320 338 350 360 370
; Generate velocites is off at 300 K.
gen_vel             =  no
gen_temp            =  300.0
gen_seed            =  173529


Temperature file:


@ s0 legend "Temperature"
    0.000000    0.086951
    0.200000  220.175079
    0.400000  262.944397
    0.600000  282.395752
    0.800000  293.998444
    1.000000  298.549774
    1.200000  300.120056
    1.400000  299.403503
    1.600000  303.405151
    1.800000  301.161957
    2.000000  304.617310
    2.200000  303.537720
    2.400000  302.279572
    2.600000  303.867737
    2.800000  302.275452
    3.000000  301.493378
    3.200000  301.526245
    3.400000  303.736694
    3.600000  301.757965
    3.800000  303.026459
    4.000000  303.397949
    4.200000  302.376648
    4.400000  303.217651
    4.600000  302.399109
    4.800000  300.652893
    5.000000  303.834076
    5.200000  301.243988
    5.400000  301.688507
    5.600000  302.610657
    5.800000  301.640869
    6.000000  304.499786
    6.200000  300.827179
    6.400000  301.871277
    6.600000  303.083862
    6.800000  301.232208
    7.000000  302.402039
    7.200000  301.419037
    7.400001  302.663788
    7.600000  302.595581
    7.800000  302.314087
    8.000000  302.684509
    8.200001  301.203461
    8.400001  302.746521
    8.600000  303.401215
    8.800000  300.715942
    9.000000  303.033508
    9.200001  303.863403
    9.400001  302.107880
    9.600000  301.958099
    9.800000  301.676819
   10.000000  300.723846


can anybody help me to soft out this problem!!

Thanks in advance. 

With prayers
Poornima


		
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