[gmx-users] energy problems

[David]

On Thu, 2004-10-07 at 17:26, Osmany Guirola Cruz wrote:
> Hi
>  I am doing a simulation of a short peptide in water with counterions Tcoup 
> Pcoup ..... but  i do a graph of the total energy and this is the result 

This could be related to the initial constraint settings *not shown in
your mdp file.
unconstrained_start =
since you generate velocities you will have to do an initial contraint
step.
Further you probably want to change your cut-offs.

I'm confused that you are allowed by grompp to have a twin range cut-off
with PME.

> 
>     t(ps)            Potencial        Kinetic                 Total       Temp        
>  0.000000  -123848.714738  24317.926256    -99530.788482  303.036540
>  0.200000  -128255.528122  26093.377899  -102162.150223  325.161236
>  0.400000  -128604.439218  25163.987820  -103440.451398  313.579691
>  0.600000  -129228.424209  24885.526342  -104342.897868  310.109658
>  0.800000  -129548.890008  24847.294010  -104701.595998  309.633228
>  1.000000  -129836.118295  25133.901220  -104702.217076  313.204769
>  .............................................
>  .......................................
>  etc
> 
> In the total energy there it's a great jump from the step(0) to the next(0.2) 
> similar in the potencial. (after this it oscillate around the averge). is 
> this correct? or i have something wrong in my mdp files 
> My TCoup=300 but g_energy say that the average is 314 that it's greater than 
> the expected value 300. Why?
>  
> here my mdp file
> title               =  fws
> cpp                 =  /usr/bin/cpp
> constraints         =  all-bonds
> integrator          =  md
> dt                  =  0.002   
> nsteps              =  5000000  
> nstcomm             =  1
> nstxout             =  5000
> nstvout             =  5000
> nstfout             =  0
> nstlist             =  10
> ns_type             =  grid
> energygrps          =  Protein  SOL
> rlist               =  0.8
> ;coulombtype            =  PME
> rcoulomb            =  1.4
> rvdw                =  0.8
> 
> ; Berendsen temperature coupling is on in three groups
> Tcoupl              =  berendsen
> tau_t               =  0.1      0.1     0.1
> tc_grps             =  protein  sol     CL-
> ref_t               =  300      300     300
> ; Pressure coupling is on
> Pcoupl              =  berendsen
> pcoupltype          =  isotropic
> tau_p               =  0.5
> compressibility     =  4.5e-5
> ref_p               =  1.0
> ; Generate velocites is on at 300 K.
> gen_vel             =  yes
> gen_temp            =  300.0
> gen_seed            =  173529
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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