normal The total potential energy is nan

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7 months 1 week ago #8925 by 若水无风
The total potential energy is nan was created by 若水无风
I am new in Martini force field and just begin with the tutorials of polymer. I have finished the steps before 'Creation of an .itp' , also i created a itp file as the tutorial told. However , when running energy minimization, the fatal error says that the total potential energy is inf. The error is as following:
Fatal error: Step -1: The total potential energy is inf, which is not finite. The LJ and electrostatic contributions to the energy are inf and 0, respectively. A non-finite potential energy can be caused by overlapping interactions in bonded interactions or very large or Nan coordinate values. Usually this is caused by a badly- or non-equilibrated initial configuration, incorrect interactions or parameters in the topology.
I have tried to modified the bond length, angle and force constant several times but didn't work. Grateful for your advise,sincerely.
PS:This is my itp file:
[ moleculetype ]
PEG9 1

[ atoms ]
; nr type resnr resid atom cgnr charge mass total_charge
1 P2 1 PEG9 H1 1 0 72
2 N0 1 PEG9 C1 2 0 72
3 N0 1 PEG9 C1 3 0 72
4 N0 1 PEG9 C1 4 0 72
5 N0 1 PEG9 C1 5 0 72
6 N0 1 PEG9 C1 6 0 72
7 N0 1 PEG9 C1 7 0 72
8 N0 1 PEG9 C1 8 0 72
9 N0 1 PEG9 C1 9 0 72
10 P2 1 PEG9 C1 10 0 72

[ bonds ]
; 1 2 1 0.470 1250
1 2 1 0.470 1250
2 3 1 0.470 1250
3 4 1 0.470 1250
4 5 1 0.470 1250
5 6 1 0.470 1250
6 7 1 0.470 1250
7 8 1 0.470 1250
8 9 1 0.470 1250
9 10 1 0.470 1250

[ angles ]
; i j k type angle force-constant
1 2 3 2 180.00 45.00
2 3 4 2 180.00 45.00
3 4 5 2 180.00 45.00
4 5 6 2 180.00 45.00
5 6 7 2 180.00 45.00
6 7 8 2 180.00 45.00
7 8 9 2 180.00 45.00
8 9 10 2 180.00 45.00

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7 months 1 week ago #8927 by vainikka
Replied by vainikka on topic The total potential energy is nan
The problem is most likely not your itp file, but your initial starting configuration. Check if you have overlapping beads.

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7 months 1 week ago - 7 months 1 week ago #8928 by 若水无风
Replied by 若水无风 on topic The total potential energy is nan
Thanks a lot for your reply, but i am a little confused about 'initial starting configuration'. If the problem dose not result from the itp or mdp file, maybe it is caused by the gro file, which was got from the last frame of the CG trajectory just following the tutorial. When i try to check the distance between the beads to find out the overlapped ones, enother error occurred.

GROMACS: gmx distance, version 2018.8
Executable: /sob/gmx2018.8/bin/gmx
Data prefix: /sob/gmx2018.8
Working dir: /mnt/hgfs/PEG_parametrization
Command line:
gmx distance -f traj_cg.xtc -len 0.35 -tol 0.8 -n bonds.ndx -oh bonds-1.xvg

Available static index groups:
Group 0 "bonds_core" (2800 atoms)
Group 1 "bonds_term" (800 atoms)
Specify any number of selections for option 'select'
(Position pairs to calculate distances for):
(one per line, <enter> for status/groups, 'help' for help, Ctrl-D to end)
> 0
Selection '0' parsed
Reading frame 0 time 20000.000 *** Error in `gmx': realloc(): invalid next size: 0x00000000015eaef0 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x7f5d4)[0x7f9fde3cf5d4]
/lib64/libc.so.6(+0x83bd8)[0x7f9fde3d3bd8]
/lib64/libc.so.6(realloc+0x1d2)[0x7f9fde3d5832]
/sob/gmx2018.8/bin/../lib64/libgromacs.so.3(save_realloc+0x34)[0x7f9fdf6b9d84]
/sob/gmx2018.8/bin/../lib64/libgromacs.so.3(_Z24gmx_ana_index_make_blockP8t_blockaPK10gmx_mtop_tP15gmx_ana_index_t9e_index_tb+0x1fd)[0x7f9fdf9cce9d]
/sob/gmx2018.8/bin/../lib64/libgromacs.so.3(+0x678808)[0x7f9fdf9f6808]
/sob/gmx2018.8/bin/../lib64/libgromacs.so.3(_Z28gmx_ana_poscalc_set_maxindexP17gmx_ana_poscalc_tP15gmx_ana_index_t+0x18)[0x7f9fdf9f7d78]
/sob/gmx2018.8/bin/../lib64/libgromacs.so.3(+0x6409ee)[0x7f9fdf9be9ee]
/sob/gmx2018.8/bin/../lib64/libgromacs.so.3(+0x6406b0)[0x7f9fdf9be6b0]
/sob/gmx2018.8/bin/../lib64/libgromacs.so.3(_ZN3gmx17SelectionCompiler7compileEPNS_19SelectionCollectionE+0x11bf)[0x7f9fdf9c2f4f]
/sob/gmx2018.8/bin/../lib64/libgromacs.so.3(_ZN3gmx19SelectionCollection7compileEv+0x80)[0x7f9fdfa050c0]
/sob/gmx2018.8/bin/../lib64/libgromacs.so.3(_ZN3gmx23SelectionOptionBehavior15optionsFinishedEv+0x395)[0x7f9fdfa0d775]
/sob/gmx2018.8/bin/../lib64/libgromacs.so.3(_ZN3gmx25OptionsBehaviorCollection15optionsFinishedEv+0xcf)[0x7f9fdfdb9dcf]
/sob/gmx2018.8/bin/../lib64/libgromacs.so.3(+0x152031)[0x7f9fdf4d0031]
/sob/gmx2018.8/bin/../lib64/libgromacs.so.3(_ZN3gmx24CommandLineModuleManager3runEiPPc+0x1eb)[0x7f9fdf4cd13b]
gmx[0x40dd5c]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7f9fde3723d5]
gmx[0x40de16]
======= Memory map: ========
00400000-00438000 r-xp 00000000 fd:00 69001098 /sob/gmx2018.8/bin/gmx
00637000-00638000 r--p 00037000 fd:00 69001098 /sob/gmx2018.8/bin/gmx
00638000-00639000 rw-p 00038000 fd:00 69001098 /sob/gmx2018.8/bin/gmx
00639000-0063a000 rw-p 00000000 00:00 0
015b3000-01609000 rw-p 00000000 00:00 0 [heap]
7f9fd8000000-7f9fd8021000 rw-p 00000000 00:00 0
7f9fd8021000-7f9fdc000000 ---p 00000000 00:00 0
7f9fddb34000-7f9fddd33000 r-xp 00000000 fd:00 68845362 /sob/fftw338/lib/libfftw3f.so.3.5.8
7f9fddd33000-7f9fddf32000 ---p 001ff000 fd:00 68845362 /sob/fftw338/lib/libfftw3f.so.3.5.8
7f9fddf32000-7f9fddf43000 r--p 001fe000 fd:00 68845362 /sob/fftw338/lib/libfftw3f.so.3.5.8
7f9fddf43000-7f9fddf44000 rw-p 0020f000 fd:00 68845362 /sob/fftw338/lib/libfftw3f.so.3.5.8
7f9fddf44000-7f9fddf4b000 r-xp 00000000 fd:00 33919727 /usr/lib64/librt-2.17.so
7f9fddf4b000-7f9fde14a000 ---p 00007000 fd:00 33919727 /usr/lib64/librt-2.17.so
7f9fde14a000-7f9fde14b000 r--p 00006000 fd:00 33919727 /usr/lib64/librt-2.17.so
7f9fde14b000-7f9fde14c000 rw-p 00007000 fd:00 33919727 /usr/lib64/librt-2.17.so
7f9fde14c000-7f9fde14e000 r-xp 00000000 fd:00 33916919 /usr/lib64/libdl-2.17.so
7f9fde14e000-7f9fde34e000 ---p 00002000 fd:00 33916919 /usr/lib64/libdl-2.17.so
7f9fde34e000-7f9fde34f000 r--p 00002000 fd:00 33916919 /usr/lib64/libdl-2.17.so
7f9fde34f000-7f9fde350000 rw-p 00003000 fd:00 33916919 /usr/lib64/libdl-2.17.so
7f9fde350000-7f9fde512000 r-xp 00000000 fd:00 33916913 /usr/lib64/libc-2.17.so
7f9fde512000-7f9fde712000 ---p 001c2000 fd:00 33916913 /usr/lib64/libc-2.17.so
7f9fde712000-7f9fde716000 r--p 001c2000 fd:00 33916913 /usr/lib64/libc-2.17.so
7f9fde716000-7f9fde718000 rw-p 001c6000 fd:00 33916913 /usr/lib64/libc-2.17.so
7f9fde718000-7f9fde71d000 rw-p 00000000 00:00 0
7f9fde71d000-7f9fde734000 r-xp 00000000 fd:00 33919723 /usr/lib64/libpthread-2.17.so
7f9fde734000-7f9fde933000 ---p 00017000 fd:00 33919723 /usr/lib64/libpthread-2.17.so
7f9fde933000-7f9fde934000 r--p 00016000 fd:00 33919723 /usr/lib64/libpthread-2.17.so
7f9fde934000-7f9fde935000 rw-p 00017000 fd:00 33919723 /usr/lib64/libpthread-2.17.so
7f9fde935000-7f9fde939000 rw-p 00000000 00:00 0
7f9fde939000-7f9fde94e000 r-xp 00000000 fd:00 33554509 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7f9fde94e000-7f9fdeb4d000 ---p 00015000 fd:00 33554509 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7f9fdeb4d000-7f9fdeb4e000 r--p 00014000 fd:00 33554509 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7f9fdeb4e000-7f9fdeb4f000 rw-p 00015000 fd:00 33554509 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7f9fdeb4f000-7f9fdeb74000 r-xp 00000000 fd:00 33800564 /usr/lib64/libgomp.so.1.0.0
7f9fdeb74000-7f9fded73000 ---p 00025000 fd:00 33800564 /usr/lib64/libgomp.so.1.0.0
7f9fded73000-7f9fded74000 r--p 00024000 fd:00 33800564 /usr/lib64/libgomp.so.1.0.0
7f9fded74000-7f9fded75000 rw-p 00025000 fd:00 33800564 /usr/lib64/libgomp.so.1.0.0
7f9fded75000-7f9fdee76000 r-xp 00000000 fd:00 33916921 /usr/lib64/libm-2.17.so
7f9fdee76000-7f9fdf075000 ---p 00101000 fd:00 33916921 /usr/lib64/libm-2.17.so
7f9fdf075000-7f9fdf076000 r--p 00100000 fd:00 33916921 /usr/lib64/libm-2.17.so
7f9fdf076000-7f9fdf077000 rw-p 00101000 fd:00 33916921 /usr/lib64/libm-2.17.so
7f9fdf077000-7f9fdf160000 r-xp 00000000 fd:00 33920962 /usr/lib64/libstdc++.so.6.0.19
7f9fdf160000-7f9fdf35f000 ---p 000e9000 fd:00 33920962 /usr/lib64/libstdc++.so.6.0.19
7f9fdf35f000-7f9fdf367000 r--p 000e8000 fd:00 33920962 /usr/lib64/libstdc++.so.6.0.19
7f9fdf367000-7f9fdf369000 rw-p 000f0000 fd:00 33920962 /usr/lib64/libstdc++.so.6.0.19
7f9fdf369000-7f9fdf37e000 rw-p 00000000 00:00 0
7f9fdf37e000-7f9fdffc7000 r-xp 00000000 fd:00 37305981 /sob/gmx2018.8/lib64/libgromacs.so.3.5.0
7f9fdffc7000-7f9fe01c7000 ---p 00c49000 fd:00 37305981 /sob/gmx2018.8/lib64/libgromacs.so.3.5.0
7f9fe01c7000-7f9fe01d8000 r--p 00c49000 fd:00 37305981 /sob/gmx2018.8/lib64/libgromacs.so.3.5.0
7f9fe01d8000-7f9fe01f8000 rw-p 00c5a000 fd:00 37305981 /sob/gmx2018.8/lib64/libgromacs.so.3.5.0
7f9fe01f8000-7f9fe01fa000 rw-p 00000000 00:00 0
7f9fe01fa000-7f9fe021c000 r-xp 00000000 fd:00 33916906 /usr/lib64/ld-2.17.so
7f9fe03fc000-7f9fe0404000 rw-p 00000000 00:00 0
7f9fe0417000-7f9fe041b000 rw-p 00000000 00:00 0
7f9fe041b000-7f9fe041c000 r--p 00021000 fd:00 33916906 /usr/lib64/ld-2.17.so
7f9fe041c000-7f9fe041d000 rw-p 00022000 fd:00 33916906 /usr/lib64/ld-2.17.so
7f9fe041d000-7f9fe041e000 rw-p 00000000 00:00 0
7ffdcd3ea000-7ffdcd40b000 rw-p 00000000 00:00 0 [stack]
7ffdcd4dc000-7ffdcd4de000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
Aborted (core dumped)
Last edit: 7 months 1 week ago by 若水无风.

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7 months 6 days ago #8930 by 若水无风
Replied by 若水无风 on topic The total potential energy is nan
Since just like vainikka said, maybe the mistakes in the gro file cause the infinite potential energy, which was got from the last frame of the CG trajectory. So i try to get the gro file from other frame of the trajectory, for example , the 99000 frame instead of the last frame of 100000, and the problem solved.
Also i am confused why the configuration of the last frame of a md trajectory is unreasonable.
About the error of gmx distance, i divided the bonds.ndx file into 'bonds-core1', 'bonds-core2', 'bonds-term',then the command could work normally. The reason is incomprehensible, too.

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1 month 3 weeks ago #9181 by saini
Replied by saini on topic The total potential energy is nan
Dear Martini users,
I am also getting the same error (Fatal error:
Step 28561400: The total potential energy is nan, which is not finite. The LJ
and electrostatic contributions to the energy are 0 and -20416.1,
respectively. A non-finite potential energy can be caused by overlapping
interactions in bonded interactions or very large or Nan coordinate values.
Usually this is caused by a badly- or non-equilibrated initial configuration,
incorrect interactions or parameters in the topology.
)
during NPT equilbration.

I have added cholrohpyll (CLA) molecules in bilayer then after energy minimization, i have running NPT equilbration.
without CLA bilayer NPT equilibration running fine without any error.

Please suggest me something how can i fix this error.

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1 month 2 weeks ago #9182 by xavier
Replied by xavier on topic The total potential energy is nan
Hi Saini,

This error is “relatively” common. It happens when a step is moving atoms a little off and the motion bad increases quickly and forces get nuts.

Often restarting the simulation using the last or previous cot is enough. Use -cpi status.cot or -cpi status _prev.cpt, respectively.
If not enough, I doubt it, you can extract a conformation with velocities from the trr file. Otherwise it might indicate that your system went bad earlier. But I doubt it.

Good luck.

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1 month 2 weeks ago #9183 by saini
Replied by saini on topic The total potential energy is nan
Thank you for your reply.
After few ns i got this error then again and aging i run the simution by using this -cpi npt.cpt -append option. Then even in production i am getting same error. Is it generally happing in CG system or i am doing somthing wrong?
this problem is coming after addition of chlorohyll molecule, without cholrophyll molecules everything is fine?

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