[gmx-users] energy problems

[Osmany Guirola Cruz]

Ok...." "
 In the simulation i am not using PME i am using cuttoff in the mdp file
the PME line have a coment .. sorry for the inclusion of this line :-(
About the cut-offs what  should i do? 
Which are the "perfect" cut-offs for MD? or How can i set this values for a 
perfect run?
Thanks  "I will add the unconstrained_start  option to my mdp file" 
Osmany

On Thursday 07 October 2004 15:54, David wrote:
> 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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