Dear Mark,<br><br>Some groups which were constrained in all 3 dimensions in one .mdp whereas in other .mdp that groups were not constrained in x-direction.<br>But now I used same .mdp file and now even "nrdf" are same.<br>
<br>Strangely (common atleast when doing this simulation), the total energy and other thermodynamics quantities were "nan" before but now they show some huge number.<br><br>One thing I observed is the simulation runs fine only once (esp. first time), but throws up error innumerous times after that. <br>
<br>I am using the same GROMACS built, same .mdp file and same values for GMXLIB (I never changed them so far)<br><br>Below are the comparison of thermodynamic comparsions<br><br>LJ (SR) step 0: 103090, step 0: 4.7561e+18<br>
Potential step 0: -707489, step 0: 4.7561e+18<br>Kinetic En. step 0: 1468.08, step 0: 1.02499e+35<br>Total Energy step 0: -706021, step 0: 1.02499e+35<br>Temperature step 0: 4.35424, step 0: 3.04006e+32<br>
Pressure (bar) step 0: -3712.49, step 0: 2.73697e+33<br>Vir-XX step 0: 44045.4, step 0: -5.41605e+20<br>Vir-XY step 0: -2748.83, step 0: 1.41247e+20<br>Vir-XZ step 0: 1057.24, step 0: 4.23707e+20<br>
Vir-YX step 0: -2800.27, step 0: 1.41247e+20<br>Vir-YY step 0: 46710.7, step 0: -1.87114e+20<br>Vir-YZ step 0: 2599.8, step 0: 1.39343e+19<br>Vir-ZX step 0: 1091.55, step 0: 4.23708e+20<br>
Vir-ZY step 0: 2549.65, step 0: 1.39336e+19<br>Vir-ZZ step 0: 49744.6, step 0: -2.84725e+21<br>Pres-XX (bar) step 0: -3489.58, step 0: 1.70507e+33<br>Pres-XY (bar) step 0: 219.836, step 0: -5.38913e+32<br>
Pres-XZ (bar) step 0: -84.925, step 0: -2.37631e+33<br>Pres-YX (bar) step 0: 223.957, step 0: -5.38913e+32<br>Pres-YY (bar) step 0: -3703.21, step 0: 2.67507e+32<br>Pres-YZ (bar) step 0: -208.473, step 0: 6.2505e+32<br>
Pres-ZX (bar) step 0: -87.6739, step 0: -2.37631e+33<br>Pres-ZY (bar) step 0: -204.455, step 0: 6.2505e+32<br>Pres-ZZ (bar) step 0: -3944.69, step 0: 6.23832e+33<br>#Surf*SurfTen step 0: -2141.58, step 0: 3.22932e+34<br>
LJ-SR:FMN-CNT step 0: -588.918, step 0: 2.06986e+18<br>LJ-SR:FMN-CMT step 0: -558.573, step 0: 1.26082e+18<br>LJ-SR:CNT-SOD step 0: -1.1571, step 0: 3.29985e+12<br>LJ-SR:CNT-SOL step 0: -305.429, step 0: 1.42541e+18<br>
LJ-SR:SOD-CMT step 0: -0.717905, step 0: 5.87209e+11<br>T-System step 0: 4.35424, step 0: 3.04006e+32<br><br><b>previously</b><br><br>LJ (SR) step 0: 103090, step 0: nan<br>
Potential step 0: -707489, step 0: nan<br>Kinetic En. step 0: 1468.08, step 0: nan<br>Total Energy step 0: -706021, step 0: nan<br>Temperature step 0: 4.35424, step 0: nan<br>
Pressure (bar) step 0: -3712.49, step 0: nan<br>Vir-XX step 0: 44045.4, step 0: nan<br>Vir-XY step 0: -2748.83, step 0: nan<br>Vir-XZ step 0: 1057.24, step 0: nan<br>
Vir-YX step 0: -2800.27, step 0: nan<br>Vir-YY step 0: 46710.7, step 0: nan<br>Vir-YZ step 0: 2599.8, step 0: nan<br>Vir-ZX step 0: 1091.55, step 0: nan<br>
Vir-ZY step 0: 2549.65, step 0: nan<br>Vir-ZZ step 0: 49744.6, step 0: nan<br>Pres-XX (bar) step 0: -3489.58, step 0: nan<br>Pres-XY (bar) step 0: 219.836, step 0: nan<br>
Pres-XZ (bar) step 0: -84.925, step 0: nan<br>Pres-YX (bar) step 0: 223.957, step 0: nan<br>Pres-YY (bar) step 0: -3703.21, step 0: nan<br>Pres-YZ (bar) step 0: -208.473, step 0: nan<br>
Pres-ZX (bar) step 0: -87.6739, step 0: nan<br>Pres-ZY (bar) step 0: -204.455, step 0: nan<br>Pres-ZZ (bar) step 0: -3944.69, step 0: nan<br>#Surf*SurfTen step 0: -2141.58, step 0: nan<br>
LJ-SR:FMN-CNT step 0: -588.918, step 0: 2.06986e+18<br>LJ-SR:FMN-CMT step 0: -558.573, step 0: 1.26082e+18<br>LJ-SR:CNT-SOD step 0: -1.1571, step 0: 3.29985e+12<br>LJ-SR:CNT-SOL step 0: -305.429, step 0: nan<br>
LJ-SR:SOD-CMT step 0: -0.717905, step 0: 5.87209e+11<br>LJ-SR:CMT-SOL step 0: -313.823, step 0: nan<br>T-System step 0: 4.35424, step 0: nan<br><br>Thanks<br>
Rajesh<br><br><br><div class="gmail_quote">On Mon, Sep 7, 2009 at 11:00 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im">Naga Rajesh Tummala wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear Mark,<br>
<br>
When I compare the .tpr files the following is the online line where its<br>
different<br>
"inputrec->grpopts.nrdf[0] (8.240200e+04 - 8.110200e+04)"<br>
</blockquote>
<br></div>
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.<br>
<br>
Did you make these .tpr files with different .mdp files? Different GMXLIB values? Different GROMACS installations?<br><font color="#888888">
<br>
Mark</font><div><div></div><div class="h5"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
When I compare two energy files,<br>
"LJ-SR:FMN-CNT step 0: -588.918, step 0: 2.06986e+18<br>
LJ-SR:FMN-CMT step 0: -558.573, step 0: 1.26082e+18<br>
LJ-SR:CNT-SOD step 0: -1.1571, step 0: 3.29985e+12<br>
LJ-SR:CNT-SOL step 0: -305.429, step 0: nan<br>
LJ-SR:SOD-CMT step 0: -0.717905, step 0: 5.87209e+11<br>
LJ-SR:CMT-SOL step 0: -313.823, step 0: nan"<br>
<br>
The total energies and also the virial, pressure, surface tension and other<br>
thermodynamics quantities are different.<br>
<br>
When I compare .trr files, there is no difference between two files in the<br>
initial step.<br>
<br>
I personally felt that there was something wrong with the force field files,<br>
but I could not find anything there.<br>
<br>
Thanks<br>
Rajesh<br>
<br>
<br>
On Mon, Sep 7, 2009 at 9:07 PM, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>wrote:<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Naga Rajesh Tummala wrote:<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear All,<br>
<br>
Two simulations runs starting from same initial configuration results in<br>
very different energies in the first step. Both are identical simulations,<br>
nothing is changed.<br>
Did anybody encounter such problem before ? If yes, can you let me know<br>
what<br>
to do to fix this problem.<br>
<br>
</blockquote>
That seems intrinsically impossible. Please use gmxcheck to compare your<br>
input and output files and report back.<br>
<br>
Mark<br>
<br>
Below are the energy outputs from 2 simulation runs. First one ran<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
smoothly<br>
for 5000 time steps where as second one crashed after 0th step.<br>
<br>
From Run 1:<br>
time: 0.00000e+00 step: 0<br>
Component Energy Av. Energy Sum Energy<br>
Bond 5.57798e+03 0.00000e+00 5.57798e+03<br>
Angle 5.60521e+03 0.00000e+00 5.60521e+03<br>
Proper Dih. 2.45557e+03 0.00000e+00 2.45557e+03<br>
LJ-14 3.58007e+03 0.00000e+00 3.58007e+03<br>
Coulomb-14 -9.18661e+02 0.00000e+00 -9.18661e+02<br>
LJ (SR) 1.03090e+05 0.00000e+00 1.03090e+05<br>
Disper. corr. -1.44859e+03 0.00000e+00 -1.44859e+03<br>
Coulomb (SR) -7.52008e+05 0.00000e+00 -7.52008e+05<br>
Coul. recip. -7.34228e+04 0.00000e+00 -7.34228e+04<br>
Potential -7.07489e+05 0.00000e+00 -7.07489e+05<br>
Kinetic En. 1.46808e+03 0.00000e+00 1.46808e+03<br>
Total Energy -7.06021e+05 0.00000e+00 -7.06021e+05<br>
Temperature 4.35424e+00 0.00000e+00 4.35424e+00<br>
Pressure (bar) -3.71249e+03 0.00000e+00 -3.71249e+03<br>
Vir-XX 4.40454e+04 0.00000e+00 4.40454e+04<br>
Vir-XY -2.74883e+03 0.00000e+00 -2.74883e+03<br>
Vir-XZ 1.05724e+03 0.00000e+00 1.05724e+03<br>
Vir-YX -2.80027e+03 0.00000e+00 -2.80027e+03<br>
Vir-YY 4.67107e+04 0.00000e+00 4.67107e+04<br>
Vir-YZ 2.59980e+03 0.00000e+00 2.59980e+03<br>
Vir-ZX 1.09155e+03 0.00000e+00 1.09155e+03<br>
Vir-ZY 2.54965e+03 0.00000e+00 2.54965e+03<br>
Vir-ZZ 4.97446e+04 0.00000e+00 4.97446e+04<br>
Pres-XX (bar) -3.48958e+03 0.00000e+00 -3.48958e+03<br>
Pres-XY (bar) 2.19836e+02 0.00000e+00 2.19836e+02<br>
Pres-XZ (bar) -8.49250e+01 0.00000e+00 -8.49250e+01<br>
Pres-YX (bar) 2.23957e+02 0.00000e+00 2.23957e+02<br>
Pres-YY (bar) -3.70321e+03 0.00000e+00 -3.70321e+03<br>
Pres-YZ (bar) -2.08473e+02 0.00000e+00 -2.08473e+02<br>
Pres-ZX (bar) -8.76739e+01 0.00000e+00 -8.76739e+01<br>
Pres-ZY (bar) -2.04455e+02 0.00000e+00 -2.04455e+02<br>
Pres-ZZ (bar) -3.94469e+03 0.00000e+00 -3.94469e+03<br>
#Surf*SurfTen -2.14158e+03 0.00000e+00 -2.14158e+03<br>
Mu-X -3.94890e+03 0.00000e+00 -3.94890e+03<br>
Mu-Y 8.47297e+00 0.00000e+00 8.47297e+00<br>
Mu-Z 3.71283e+02 0.00000e+00 3.71283e+02<br>
Coul-SR:FMN-FMN 1.65804e+04 0.00000e+00 1.65804e+04<br>
LJ-SR:FMN-FMN -4.43681e+03 0.00000e+00 -4.43681e+03<br>
Coul-14:FMN-FMN -9.18661e+02 0.00000e+00 -9.18661e+02<br>
LJ-14:FMN-FMN 3.58007e+03 0.00000e+00 3.58007e+03<br>
*LJ-SR:FMN-CNT -5.88918e+02 0.00000e+00 -5.88918e+02*<br>
Coul-SR:FMN-SOD -8.47612e+04 0.00000e+00 -8.47612e+04<br>
LJ-SR:FMN-SOD 4.93246e+02 0.00000e+00 4.93246e+02<br>
LJ-SR:FMN-CMT -5.58573e+02 0.00000e+00 -5.58573e+02<br>
Coul-SR:FMN-SOL -2.41537e+04 0.00000e+00 -2.41537e+04<br>
LJ-SR:FMN-SOL -4.60796e+03 0.00000e+00 -4.60796e+03<br>
LJ-SR:CNT-SOD -1.15710e+00 0.00000e+00 -1.15710e+00<br>
LJ-SR:CNT-SOL -3.05429e+02 0.00000e+00 -3.05429e+02<br>
Coul-SR:SOD-SOD 2.04577e+04 0.00000e+00 2.04577e+04<br>
LJ-SR:SOD-SOD -2.29117e+01 0.00000e+00 -2.29117e+01<br>
LJ-SR:SOD-CMT -7.17905e-01 0.00000e+00 -7.17905e-01<br>
Coul-SR:SOD-SOL -1.84476e+04 0.00000e+00 -1.84476e+04<br>
LJ-SR:SOD-SOL 1.89181e+03 0.00000e+00 1.89181e+03<br>
LJ-SR:CMT-SOL -3.13823e+02 0.00000e+00 -3.13823e+02<br>
Coul-SR:SOL-SOL -6.61683e+05 0.00000e+00 -6.61683e+05<br>
LJ-SR:SOL-SOL 1.11541e+05 0.00000e+00 1.11541e+05<br>
T-System 4.35424e+00 0.00000e+00 4.35424e+00<br>
Xi-System 0.00000e+00 0.00000e+00 0.00000e+00<br>
<br>
From Run 2:<br>
time: 0.00000e+00 step: 0<br>
Component Energy Av. Energy Sum Energy<br>
Bond 5.57798e+03 0.00000e+00 5.57798e+03<br>
Angle 5.60521e+03 0.00000e+00 5.60521e+03<br>
Proper Dih. 2.45557e+03 0.00000e+00 2.45557e+03<br>
LJ-14 3.58007e+03 0.00000e+00 3.58007e+03<br>
Coulomb-14 -9.18661e+02 0.00000e+00 -9.18661e+02<br>
LJ (SR) 4.75610e+18 0.00000e+00 4.75610e+18<br>
Disper. corr. -1.44859e+03 0.00000e+00 -1.44859e+03<br>
Coulomb (SR) -7.52008e+05 0.00000e+00 -7.52008e+05<br>
Coul. recip. -7.34228e+04 0.00000e+00 -7.34228e+04<br>
Potential 4.75610e+18 0.00000e+00 4.75610e+18<br>
Kinetic En. 1.17875e+35 0.00000e+00 1.17875e+35<br>
Total Energy 1.17875e+35 0.00000e+00 1.17875e+35<br>
Temperature 3.44094e+32 0.00000e+00 3.44094e+32<br>
Pressure (bar) 3.14754e+33 0.00000e+00 3.14754e+33<br>
Vir-XX -5.41605e+20 0.00000e+00 -5.41605e+20<br>
Vir-XY 1.41247e+20 0.00000e+00 1.41247e+20<br>
Vir-XZ 4.23707e+20 0.00000e+00 4.23707e+20<br>
Vir-YX 1.41247e+20 0.00000e+00 1.41247e+20<br>
Vir-YY -1.87114e+20 0.00000e+00 -1.87114e+20<br>
Vir-YZ 1.39343e+19 0.00000e+00 1.39343e+19<br>
Vir-ZX 4.23708e+20 0.00000e+00 4.23708e+20<br>
Vir-ZY 1.39336e+19 0.00000e+00 1.39336e+19<br>
Vir-ZZ -2.84725e+21 0.00000e+00 -2.84725e+21<br>
Pres-XX (bar) 2.93679e+33 0.00000e+00 2.93679e+33<br>
Pres-XY (bar) -5.38913e+32 0.00000e+00 -5.38913e+32<br>
Pres-XZ (bar) -2.37631e+33 0.00000e+00 -2.37631e+33<br>
Pres-YX (bar) -5.38913e+32 0.00000e+00 -5.38913e+32<br>
Pres-YY (bar) 2.67507e+32 0.00000e+00 2.67507e+32<br>
Pres-YZ (bar) 6.25050e+32 0.00000e+00 6.25050e+32<br>
Pres-ZX (bar) -2.37631e+33 0.00000e+00 -2.37631e+33<br>
Pres-ZY (bar) 6.25050e+32 0.00000e+00 6.25050e+32<br>
Pres-ZZ (bar) 6.23832e+33 0.00000e+00 6.23832e+33<br>
#Surf*SurfTen 2.85064e+34 0.00000e+00 2.85064e+34<br>
Mu-X -3.94890e+03 0.00000e+00 -3.94890e+03<br>
Mu-Y 8.47297e+00 0.00000e+00 8.47297e+00<br>
Mu-Z 3.71283e+02 0.00000e+00 3.71283e+02<br>
Coul-SR:FMN-FMN 1.65804e+04 0.00000e+00 1.65804e+04<br>
LJ-SR:FMN-FMN -4.43681e+03 0.00000e+00 -4.43681e+03<br>
Coul-14:FMN-FMN -9.18661e+02 0.00000e+00 -9.18661e+02<br>
LJ-14:FMN-FMN 3.58007e+03 0.00000e+00 3.58007e+03<br>
* LJ-SR:FMN-CNT 2.06986e+18 0.00000e+00 2.06986e+18*<br>
Coul-SR:FMN-SOD -8.47612e+04 0.00000e+00 -8.47612e+04<br>
LJ-SR:FMN-SOD 4.93246e+02 0.00000e+00 4.93246e+02<br>
LJ-SR:FMN-CMT 1.26082e+18 0.00000e+00 1.26082e+18<br>
Coul-SR:FMN-SOL -2.41537e+04 0.00000e+00 -2.41537e+04<br>
LJ-SR:FMN-SOL -4.60796e+03 0.00000e+00 -4.60796e+03<br>
LJ-SR:CNT-SOD 3.29985e+12 0.00000e+00 3.29985e+12<br>
LJ-SR:CNT-SOL 1.42541e+18 0.00000e+00 1.42541e+18<br>
Coul-SR:SOD-SOD 2.04577e+04 0.00000e+00 2.04577e+04<br>
LJ-SR:SOD-SOD -2.29117e+01 0.00000e+00 -2.29117e+01<br>
LJ-SR:SOD-CMT 5.87209e+11 0.00000e+00 5.87209e+11<br>
Coul-SR:SOD-SOL -1.84476e+04 0.00000e+00 -1.84476e+04<br>
LJ-SR:SOD-SOL 1.89181e+03 0.00000e+00 1.89181e+03<br>
LJ-SR:CMT-SOL -3.13899e+02 0.00000e+00 -3.13899e+02<br>
Coul-SR:SOL-SOL -6.61683e+05 0.00000e+00 -6.61683e+05<br>
LJ-SR:SOL-SOL 1.11541e+05 0.00000e+00 1.11541e+05<br>
T-System 3.44094e+32 0.00000e+00 3.44094e+32<br>
Xi-System 0.00000e+00 0.00000e+00 0.00000e+00<br>
<br>
Thanks a lot<br>
Any help is greatly appreciated.<br>
<br>
Thanks<br>
Rajesh<br>
<br>
<br>
<br>
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