Hi Developers
I am using plumed for trajectory analysis. I want to calculate radius of
Gyration on C-alpha atom.
For this I make a input file plumed.dat file as following:
r: GYRATION ATOM=9, 28, 40, 61, 68, 79, 89, 113, 123, 133, 143, 153,
163, 180, 191, 215, 236, 243, 255, 274, 284, 295, 314, 331, 338, 348,
355, 365, 375, 390, 396, 403, 414, 421, 440, 446, 457, 467, 477, 487,
498, 509, 520, 544, 561, 575, 594, 614, 628, 638, 653, 668, 675, 692,
711, 732
Then I run it with the following command:
plumed driver --plumed plumed.dat --mf_crd md.mdcrd --natoms 30769
But it gives me the error:
DRIVER: Found molfile format trajectory crd with name md.mdcrd
Problem reading CRD file
PLUMED:
PLUMED:
################################################################################
PLUMED:
PLUMED: (core/PlumedMain.cpp:618) virtual void
PLMD::PlumedMain::cmd(const string&, const PLMD::TypesafePtr&)
PLUMED: +++ assertion failed: initialized
PLUMED: cmd("runFinalJobs") should be only used after plumed
initialization
PLUMED:
################################################################################
PLUMED: Cycles
Total Average Minimum Maximum
PLUMED: 1
0.000130 0.000130 0.000130 0.000130
terminate called after throwing an instance of
'PLMD::Plumed::ExceptionError'
what():
(core/PlumedMain.cpp:618) virtual void PLMD::PlumedMain::cmd(const
string&, const PLMD::TypesafePtr&)
+++ assertion failed: initialized
cmd("runFinalJobs") should be only used after plumed initialization
[pluto:900899] *** Process received signal ***
[pluto:900899] Signal: Aborted (6)
[pluto:900899] Signal code: (-6)
[pluto:900899] [ 0] /lib64/libpthread.so.0(+0x12cf0)[0x7f2bca099cf0]
[pluto:900899] [ 1] /lib64/libc.so.6(gsignal+0x10f)[0x7f2bc9d10acf]
[pluto:900899] [ 2] /lib64/libc.so.6(abort+0x127)[0x7f2bc9ce3ea5]
[pluto:900899] [ 3] /lib64/libstdc++.so.6(+0x9009b)[0x7f2bca8d109b]
[pluto:900899] [ 4] /lib64/libstdc++.so.6(+0x9654c)[0x7f2bca8d754c]
[pluto:900899] [ 5] /lib64/libstdc++.so.6(+0x965a7)[0x7f2bca8d75a7]
[pluto:900899] [ 6]
/lib64/libstdc++.so.6(__cxa_rethrow+0x4d)[0x7f2bca8d785d]
[pluto:900899] [ 7] plumed[0x4053e1]
[pluto:900899] [ 8]
/lib64/libc.so.6(__libc_start_main+0xe5)[0x7f2bc9cfcd85]
[pluto:900899] [ 9] plumed[0x40560e]
[pluto:900899] *** End of error message ***
Aborted (core dumped)
Please help me to understand why I'm getting this error.
Munazzah
Ph.D scholar
RRCAT Indore,
M.P. India
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Received on Thu Dec 07 2023 - 03:30:02 PST
