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

[Fahimeh Baftizadeh]

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...

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
> > --
> > gmx-users mailing list
>
> > gmx-users@
>
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > * Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to
>
> > gmx-users-request@
>
> > .
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
>
>
> --
> 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.
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
---------------------------------------------------------------------------------------------------
"If you torture the data long enough, they will confess to anything!" John
Tukey