Naga Rajesh Tummala wrote:
Dear Mark,
Some groups which were constrained in all 3 dimensions in one .mdp
whereas in other .mdp that groups were not constrained in x-direction.
But now I used same .mdp file and now even "nrdf" are same.
Strangely (common atleast when doing this simulation), the total energy
and other thermodynamics quantities were "nan" before but now they show
some huge number.
One thing I observed is the simulation runs fine only once (esp. first
time), but throws up error innumerous times after that.
I am using the same GROMACS built, same .mdp file and same values for
GMXLIB (I never changed them so far)
Below are the comparison of thermodynamic comparsions
LJ (SR) step 0: 103090, step 0: 4.7561e+18
Potential step 0: -707489, step 0: 4.7561e+18
Kinetic En. step 0: 1468.08, step 0: 1.02499e+35
Total Energy step 0: -706021, step 0: 1.02499e+35
Temperature step 0: 4.35424, step 0: 3.04006e+32
Pressure (bar) step 0: -3712.49, step 0: 2.73697e+33
Vir-XX step 0: 44045.4, step 0: -5.41605e+20
Vir-XY step 0: -2748.83, step 0: 1.41247e+20
Vir-XZ step 0: 1057.24, step 0: 4.23707e+20
Vir-YX step 0: -2800.27, step 0: 1.41247e+20
Vir-YY step 0: 46710.7, step 0: -1.87114e+20
Vir-YZ step 0: 2599.8, step 0: 1.39343e+19
Vir-ZX step 0: 1091.55, step 0: 4.23708e+20
Vir-ZY step 0: 2549.65, step 0: 1.39336e+19
Vir-ZZ step 0: 49744.6, step 0: -2.84725e+21
Pres-XX (bar) step 0: -3489.58, step 0: 1.70507e+33
Pres-XY (bar) step 0: 219.836, step 0: -5.38913e+32
Pres-XZ (bar) step 0: -84.925, step 0: -2.37631e+33
Pres-YX (bar) step 0: 223.957, step 0: -5.38913e+32
Pres-YY (bar) step 0: -3703.21, step 0: 2.67507e+32
Pres-YZ (bar) step 0: -208.473, step 0: 6.2505e+32
Pres-ZX (bar) step 0: -87.6739, step 0: -2.37631e+33
Pres-ZY (bar) step 0: -204.455, step 0: 6.2505e+32
Pres-ZZ (bar) step 0: -3944.69, step 0: 6.23832e+33
#Surf*SurfTen step 0: -2141.58, step 0: 3.22932e+34
LJ-SR:FMN-CNT step 0: -588.918, step 0: 2.06986e+18
LJ-SR:FMN-CMT step 0: -558.573, step 0: 1.26082e+18
LJ-SR:CNT-SOD step 0: -1.1571, step 0: 3.29985e+12
LJ-SR:CNT-SOL step 0: -305.429, step 0: 1.42541e+18
LJ-SR:SOD-CMT step 0: -0.717905, step 0: 5.87209e+11
T-System step 0: 4.35424, step 0: 3.04006e+32
*previously*
LJ (SR) step 0: 103090, step 0: nan
Potential step 0: -707489, step 0: nan
Kinetic En. step 0: 1468.08, step 0: nan
Total Energy step 0: -706021, step 0: nan
Temperature step 0: 4.35424, step 0: nan
Pressure (bar) step 0: -3712.49, step 0: nan
Vir-XX step 0: 44045.4, step 0: nan
Vir-XY step 0: -2748.83, step 0: nan
Vir-XZ step 0: 1057.24, step 0: nan
Vir-YX step 0: -2800.27, step 0: nan
Vir-YY step 0: 46710.7, step 0: nan
Vir-YZ step 0: 2599.8, step 0: nan
Vir-ZX step 0: 1091.55, step 0: nan
Vir-ZY step 0: 2549.65, step 0: nan
Vir-ZZ step 0: 49744.6, step 0: nan
Pres-XX (bar) step 0: -3489.58, step 0: nan
Pres-XY (bar) step 0: 219.836, step 0: nan
Pres-XZ (bar) step 0: -84.925, step 0: nan
Pres-YX (bar) step 0: 223.957, step 0: nan
Pres-YY (bar) step 0: -3703.21, step 0: nan
Pres-YZ (bar) step 0: -208.473, step 0: nan
Pres-ZX (bar) step 0: -87.6739, step 0: nan
Pres-ZY (bar) step 0: -204.455, step 0: nan
Pres-ZZ (bar) step 0: -3944.69, step 0: nan
#Surf*SurfTen step 0: -2141.58, step 0: nan
LJ-SR:FMN-CNT step 0: -588.918, step 0: 2.06986e+18
LJ-SR:FMN-CMT step 0: -558.573, step 0: 1.26082e+18
LJ-SR:CNT-SOD step 0: -1.1571, step 0: 3.29985e+12
LJ-SR:CNT-SOL step 0: -305.429, step 0: nan
LJ-SR:SOD-CMT step 0: -0.717905, step 0: 5.87209e+11
LJ-SR:CMT-SOL step 0: -313.823, step 0: nan
T-System step 0: 4.35424, step 0: nan
It looks to me like you have severe atomic overlap between these two systems
(and hence the astronomically large values for short-range nonbonded
parameters). Have you done any sort of energy minimization and equilibration on
this system?
-Justin
Thanks
Rajesh
On Mon, Sep 7, 2009 at 11:00 PM, Mark Abraham <[email protected]
<mailto:[email protected]>> wrote:
Naga Rajesh Tummala wrote:
Dear Mark,
When I compare the .tpr files the following is the online line
where its
different
"inputrec->grpopts.nrdf[0] (8.240200e+04 - 8.110200e+04)"
IIRC "nrdf" is short for "number of degrees of freedom" which in
turn suggests that the number of constraints has changed between the
files, but I don't know if that's consistent with all other .tpr
entries being identical.
Did you make these .tpr files with different .mdp files? Different
GMXLIB values? Different GROMACS installations?
Mark
When I compare two energy files,
"LJ-SR:FMN-CNT step 0: -588.918, step 0: 2.06986e+18
LJ-SR:FMN-CMT step 0: -558.573, step 0: 1.26082e+18
LJ-SR:CNT-SOD step 0: -1.1571, step 0: 3.29985e+12
LJ-SR:CNT-SOL step 0: -305.429, step 0: nan
LJ-SR:SOD-CMT step 0: -0.717905, step 0: 5.87209e+11
LJ-SR:CMT-SOL step 0: -313.823, step 0: nan"
The total energies and also the virial, pressure, surface
tension and other
thermodynamics quantities are different.
When I compare .trr files, there is no difference between two
files in the
initial step.
I personally felt that there was something wrong with the force
field files,
but I could not find anything there.
Thanks
Rajesh
On Mon, Sep 7, 2009 at 9:07 PM, Mark Abraham
<[email protected] <mailto:[email protected]>>wrote:
Naga Rajesh Tummala wrote:
Dear All,
Two simulations runs starting from same initial
configuration results in
very different energies in the first step. Both are
identical simulations,
nothing is changed.
Did anybody encounter such problem before ? If yes, can
you let me know
what
to do to fix this problem.
That seems intrinsically impossible. Please use gmxcheck to
compare your
input and output files and report back.
Mark
Below are the energy outputs from 2 simulation runs. First
one ran
smoothly
for 5000 time steps where as second one crashed after
0th step.
From Run 1:
time: 0.00000e+00 step:
0
Component Energy Av. Energy
Sum Energy
Bond 5.57798e+03 0.00000e+00
5.57798e+03
Angle 5.60521e+03 0.00000e+00
5.60521e+03
Proper Dih. 2.45557e+03 0.00000e+00
2.45557e+03
LJ-14 3.58007e+03 0.00000e+00
3.58007e+03
Coulomb-14 -9.18661e+02 0.00000e+00
-9.18661e+02
LJ (SR) 1.03090e+05 0.00000e+00
1.03090e+05
Disper. corr. -1.44859e+03 0.00000e+00
-1.44859e+03
Coulomb (SR) -7.52008e+05 0.00000e+00
-7.52008e+05
Coul. recip. -7.34228e+04 0.00000e+00
-7.34228e+04
Potential -7.07489e+05 0.00000e+00
-7.07489e+05
Kinetic En. 1.46808e+03 0.00000e+00
1.46808e+03
Total Energy -7.06021e+05 0.00000e+00
-7.06021e+05
Temperature 4.35424e+00 0.00000e+00
4.35424e+00
Pressure (bar) -3.71249e+03 0.00000e+00
-3.71249e+03
Vir-XX 4.40454e+04 0.00000e+00
4.40454e+04
Vir-XY -2.74883e+03 0.00000e+00
-2.74883e+03
Vir-XZ 1.05724e+03 0.00000e+00
1.05724e+03
Vir-YX -2.80027e+03 0.00000e+00
-2.80027e+03
Vir-YY 4.67107e+04 0.00000e+00
4.67107e+04
Vir-YZ 2.59980e+03 0.00000e+00
2.59980e+03
Vir-ZX 1.09155e+03 0.00000e+00
1.09155e+03
Vir-ZY 2.54965e+03 0.00000e+00
2.54965e+03
Vir-ZZ 4.97446e+04 0.00000e+00
4.97446e+04
Pres-XX (bar) -3.48958e+03 0.00000e+00
-3.48958e+03
Pres-XY (bar) 2.19836e+02 0.00000e+00
2.19836e+02
Pres-XZ (bar) -8.49250e+01 0.00000e+00
-8.49250e+01
Pres-YX (bar) 2.23957e+02 0.00000e+00
2.23957e+02
Pres-YY (bar) -3.70321e+03 0.00000e+00
-3.70321e+03
Pres-YZ (bar) -2.08473e+02 0.00000e+00
-2.08473e+02
Pres-ZX (bar) -8.76739e+01 0.00000e+00
-8.76739e+01
Pres-ZY (bar) -2.04455e+02 0.00000e+00
-2.04455e+02
Pres-ZZ (bar) -3.94469e+03 0.00000e+00
-3.94469e+03
#Surf*SurfTen -2.14158e+03 0.00000e+00
-2.14158e+03
Mu-X -3.94890e+03 0.00000e+00
-3.94890e+03
Mu-Y 8.47297e+00 0.00000e+00
8.47297e+00
Mu-Z 3.71283e+02 0.00000e+00
3.71283e+02
Coul-SR:FMN-FMN 1.65804e+04 0.00000e+00
1.65804e+04
LJ-SR:FMN-FMN -4.43681e+03 0.00000e+00
-4.43681e+03
Coul-14:FMN-FMN -9.18661e+02 0.00000e+00
-9.18661e+02
LJ-14:FMN-FMN 3.58007e+03 0.00000e+00
3.58007e+03
*LJ-SR:FMN-CNT -5.88918e+02 0.00000e+00
-5.88918e+02*
Coul-SR:FMN-SOD -8.47612e+04 0.00000e+00
-8.47612e+04
LJ-SR:FMN-SOD 4.93246e+02 0.00000e+00
4.93246e+02
LJ-SR:FMN-CMT -5.58573e+02 0.00000e+00
-5.58573e+02
Coul-SR:FMN-SOL -2.41537e+04 0.00000e+00
-2.41537e+04
LJ-SR:FMN-SOL -4.60796e+03 0.00000e+00
-4.60796e+03
LJ-SR:CNT-SOD -1.15710e+00 0.00000e+00
-1.15710e+00
LJ-SR:CNT-SOL -3.05429e+02 0.00000e+00
-3.05429e+02
Coul-SR:SOD-SOD 2.04577e+04 0.00000e+00
2.04577e+04
LJ-SR:SOD-SOD -2.29117e+01 0.00000e+00
-2.29117e+01
LJ-SR:SOD-CMT -7.17905e-01 0.00000e+00
-7.17905e-01
Coul-SR:SOD-SOL -1.84476e+04 0.00000e+00
-1.84476e+04
LJ-SR:SOD-SOL 1.89181e+03 0.00000e+00
1.89181e+03
LJ-SR:CMT-SOL -3.13823e+02 0.00000e+00
-3.13823e+02
Coul-SR:SOL-SOL -6.61683e+05 0.00000e+00
-6.61683e+05
LJ-SR:SOL-SOL 1.11541e+05 0.00000e+00
1.11541e+05
T-System 4.35424e+00 0.00000e+00
4.35424e+00
Xi-System 0.00000e+00 0.00000e+00
0.00000e+00
From Run 2:
time: 0.00000e+00 step:
0
Component Energy Av. Energy
Sum Energy
Bond 5.57798e+03 0.00000e+00
5.57798e+03
Angle 5.60521e+03 0.00000e+00
5.60521e+03
Proper Dih. 2.45557e+03 0.00000e+00
2.45557e+03
LJ-14 3.58007e+03 0.00000e+00
3.58007e+03
Coulomb-14 -9.18661e+02 0.00000e+00
-9.18661e+02
LJ (SR) 4.75610e+18 0.00000e+00
4.75610e+18
Disper. corr. -1.44859e+03 0.00000e+00
-1.44859e+03
Coulomb (SR) -7.52008e+05 0.00000e+00
-7.52008e+05
Coul. recip. -7.34228e+04 0.00000e+00
-7.34228e+04
Potential 4.75610e+18 0.00000e+00
4.75610e+18
Kinetic En. 1.17875e+35 0.00000e+00
1.17875e+35
Total Energy 1.17875e+35 0.00000e+00
1.17875e+35
Temperature 3.44094e+32 0.00000e+00
3.44094e+32
Pressure (bar) 3.14754e+33 0.00000e+00
3.14754e+33
Vir-XX -5.41605e+20 0.00000e+00
-5.41605e+20
Vir-XY 1.41247e+20 0.00000e+00
1.41247e+20
Vir-XZ 4.23707e+20 0.00000e+00
4.23707e+20
Vir-YX 1.41247e+20 0.00000e+00
1.41247e+20
Vir-YY -1.87114e+20 0.00000e+00
-1.87114e+20
Vir-YZ 1.39343e+19 0.00000e+00
1.39343e+19
Vir-ZX 4.23708e+20 0.00000e+00
4.23708e+20
Vir-ZY 1.39336e+19 0.00000e+00
1.39336e+19
Vir-ZZ -2.84725e+21 0.00000e+00
-2.84725e+21
Pres-XX (bar) 2.93679e+33 0.00000e+00
2.93679e+33
Pres-XY (bar) -5.38913e+32 0.00000e+00
-5.38913e+32
Pres-XZ (bar) -2.37631e+33 0.00000e+00
-2.37631e+33
Pres-YX (bar) -5.38913e+32 0.00000e+00
-5.38913e+32
Pres-YY (bar) 2.67507e+32 0.00000e+00
2.67507e+32
Pres-YZ (bar) 6.25050e+32 0.00000e+00
6.25050e+32
Pres-ZX (bar) -2.37631e+33 0.00000e+00
-2.37631e+33
Pres-ZY (bar) 6.25050e+32 0.00000e+00
6.25050e+32
Pres-ZZ (bar) 6.23832e+33 0.00000e+00
6.23832e+33
#Surf*SurfTen 2.85064e+34 0.00000e+00
2.85064e+34
Mu-X -3.94890e+03 0.00000e+00
-3.94890e+03
Mu-Y 8.47297e+00 0.00000e+00
8.47297e+00
Mu-Z 3.71283e+02 0.00000e+00
3.71283e+02
Coul-SR:FMN-FMN 1.65804e+04 0.00000e+00
1.65804e+04
LJ-SR:FMN-FMN -4.43681e+03 0.00000e+00
-4.43681e+03
Coul-14:FMN-FMN -9.18661e+02 0.00000e+00
-9.18661e+02
LJ-14:FMN-FMN 3.58007e+03 0.00000e+00
3.58007e+03
* LJ-SR:FMN-CNT 2.06986e+18 0.00000e+00
2.06986e+18*
Coul-SR:FMN-SOD -8.47612e+04 0.00000e+00
-8.47612e+04
LJ-SR:FMN-SOD 4.93246e+02 0.00000e+00
4.93246e+02
LJ-SR:FMN-CMT 1.26082e+18 0.00000e+00
1.26082e+18
Coul-SR:FMN-SOL -2.41537e+04 0.00000e+00
-2.41537e+04
LJ-SR:FMN-SOL -4.60796e+03 0.00000e+00
-4.60796e+03
LJ-SR:CNT-SOD 3.29985e+12 0.00000e+00
3.29985e+12
LJ-SR:CNT-SOL 1.42541e+18 0.00000e+00
1.42541e+18
Coul-SR:SOD-SOD 2.04577e+04 0.00000e+00
2.04577e+04
LJ-SR:SOD-SOD -2.29117e+01 0.00000e+00
-2.29117e+01
LJ-SR:SOD-CMT 5.87209e+11 0.00000e+00
5.87209e+11
Coul-SR:SOD-SOL -1.84476e+04 0.00000e+00
-1.84476e+04
LJ-SR:SOD-SOL 1.89181e+03 0.00000e+00
1.89181e+03
LJ-SR:CMT-SOL -3.13899e+02 0.00000e+00
-3.13899e+02
Coul-SR:SOL-SOL -6.61683e+05 0.00000e+00
-6.61683e+05
LJ-SR:SOL-SOL 1.11541e+05 0.00000e+00
1.11541e+05
T-System 3.44094e+32 0.00000e+00
3.44094e+32
Xi-System 0.00000e+00 0.00000e+00
0.00000e+00
Thanks a lot
Any help is greatly appreciated.
Thanks
Rajesh
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list [email protected]
<mailto:[email protected]>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the list.
Use the www
interface or send it to [email protected]
<mailto:[email protected]>.
Can't post? Read
http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list [email protected]
<mailto:[email protected]>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search
before posting!
Please don't post (un)subscribe requests to the list. Use
the www interface
or send it to [email protected]
<mailto:[email protected]>.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list [email protected]
<mailto:[email protected]>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search
before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected]
<mailto:[email protected]>.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list [email protected]
<mailto:[email protected]>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to [email protected]
<mailto:[email protected]>.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
