[gmx-users] energy problems
Osmany Guirola Cruz
osmany.guirola at cigb.edu.cu
Thu Oct 7 23:35:57 CEST 2004
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
Thanks "I will add the unconstrained_start option to my mdp file"
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
> 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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