[gmx-users] Re: Different energy using the identical tpr file
Fahimeh Baftizadeh
fahimeh.baftizadeh at googlemail.com
Fri Apr 19 19:34:12 CEST 2013
Dear Mark,
Thanks for the pages.
Now it is clear to me that because the shared libraries maybe are not
identical during compilation, I am getting different value for energies.
However, I have to perform single point energy calculation for a lot of
structure and the only thing that I care about is the energy difference. I
have checked the energy difference that I get in different computers ...
casue I thought that maybe the difference is identical. However this is not
the case as well ...
May I have your comment about it?
E2-E1(computer1)= 83801.086088
E2-E1(computer2)= 8366.248918
As you see the order of magnitude is even different !
Could you please help me to understand this better
Thanks
Fahimeh
On Fri, Apr 19, 2013 at 9:01 AM, Mark Abraham <mark.j.abraham at gmail.com>wrote:
> 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
> > > > --
> > > > 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
> > --
> > 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
> --
> 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
More information about the gromacs.org_gmx-users
mailing list