[gmx-users] Re: Different energy using the identical tpr file
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 listgmx-users@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Different energy using the identical tpr file
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= 1000
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 are...@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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Re: [gmx-users] Re: Different energy using the identical tpr file
On Apr 19, 2013 2:50 PM, Fahimeh Baftizadeh
fahimeh.baftiza...@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= 1000
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 are...@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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Tukey
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Re: [gmx-users] Re: Different energy using the identical tpr file
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.abra...@gmail.comwrote:
On Apr 19, 2013 2:50 PM, Fahimeh Baftizadeh
fahimeh.baftiza...@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= 1000
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 are...@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
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http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
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* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to
gmx-users-request@
.
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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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If you torture the data long
