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

Wed Mar 29 14:57:23 CEST 2006

Dear Peter,

  Thank you very much for your reply. I agree that I did spelling mistake in this MD mdp file. But I tried two more MD runs with simulated annealing. One from the manual (example parameters I used) and the another one in which I gave the parameters on my own. But in both the cases there is no spelling mistake.  But When I run the grompp program it shows warning for the simulated annealing parameters and runs with the reference temperature as I mentioned in my previous mail.  

  Thanks once again,

  With prayers
  Poornima

Peter Friedel <friedel at ipfdd.de> wrote:
  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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