[gmx-users] Re: Different energy using the identical tpr file

[Mark Abraham]

On Apr 19, 2013 2:50 PM, "Fahimeh Baftizadeh" <
fahimeh.baftizadeh at googlemail.com> wrote:
>
> Hi thanks for your reply, and sorry to be late since I am living 9 hours
> behind you :)
>
> I tried but still I get different energies. I check tpr files, according
to
> gmxcheck they are identical ...
> But they give me different energies in different computers...

I didn't write and link those pages for my own benefit ;-)

Mark

>
> here is what I do:
>
> $Mygrompp -f nvt.mdp -c out.pdb -p gromacs-complex-dman-par.top -o
test0.tpr
> $Mymdrun -deffnm test0 -s test0.tpr -rerun out.pdb -reprod
> rm -f *.xvg
> echo 10 0 | $Mygenergy -f test0.edr -o energy.xvg
> cat energy.xvg | tail -1 | awk '{print $2}' >> Out-enegy
>
> And this is the content of nvt.mdp
>
> title                    = polyala
> cpp                      = /usr/bin/cpp
> integrator               = md
> comm_mode                = Linear
> dt                       = 0.002
> nsteps                   = 0
>
> nstxout                  = 1
> nstvout                  = 1
>
> nstlog                   = 1
> nstenergy                = 1
> nstxtcout                = 1
> xtc-precision            = 10000000
> energygrps               = System
>
> pbc                      = xyz
>
> nstlist                  = 10
> ns_type                  = grid
> rlist                    = 0.9
>
> coulombtype              = PME
> rcoulomb                 = 0.9
> fourierspacing           = 0.12
> pme_order                = 4
> ewald_rtol               = 1e-5
> epsilon_r                = 1.0
> optimize_fft             = yes
>
> vdwtype                  = Cut-off
> rvdw                     = 0.9
>
> ; T coupling
> tcoupl                   = Nose-Hoover
> tc-grps                  = System
> tau_t                    = 1
> ref_t                    = 300.0
>
> ; P coupling
> pcoupl                   = no
> pcoupltype               = isotropic
> tau_p                    = 1
> compressibility          = 4.5e-5
> ref_p                    = 1.0
>
> ; Velocity generation
> gen_vel                  = no
> gen_temp                 = 350.0
> gen_seed                 = 13200
>
> ; Constraints bonds
> constraints              = all-bonds
> constraint_algorithm     = lincs
> lincs-order              = 4
> lincs-warnangle          = 30
> user1-grps               = System
>
>
>
>
>
> On Fri, Apr 19, 2013 at 6:15 AM, Andrish Reddy <areddy at csir.co.za> wrote:
>
> > Have you tried the -reprod option?
> >
> > Andrish
> >
> >
> > Fahimeh Baftizadeh wrote
> > > Hello,
> > >
> > > I have a 2 tpr files which are identical. Then I am doing a single
step
> > MD
> > > (I put n_step=0) simulation just to compute the total energy of a
certain
> > > configuration.
> > >
> > > These tpr files give me different energy values ... when I run it on
my
> > > computer or on another computer. Even the gromacs version is the same
in
> > > both computers. I compiled gromacs identical in both computers.
> > >
> > > Can you help me to figure it out?
> > > Thanks
> > > Fahimeh
> > > --
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> >
> >
> > --
> > View this message in context:
> >
http://gromacs.5086.x6.nabble.com/Different-energy-using-the-identical-tpr-file-tp5007436p5007441.html
> > Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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---------------------------------------------------------------------------------------------------
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