Munazzah,
I'm afraid I have to defer to someone else on suggestions - btw, did you
try what Daniel suggested? - as appears that the problems are with the
plumed driver and/or mdtraj.
As you state, the issue is that the plumed driver cannot read an AMBER
mdcrd file. It is telling that the plumed driver works with the mdcrd file
after conversion to another format (xtc, which is lower precision among
other things).
This is not to say that it couldn't be upstream with AMBER itself, but you
are passing the AMBER-generated file through (at least) 2 different pieces
of software down the line.
I strongly suggest you reach out to the plumed community for an assist as
you eliminate variables from what's causing the problem.
Cheers,
Todd
On Fri, Dec 8, 2023 at 12:45 AM <munazzah.rrcat.gov.in> wrote:
> Hi Todd,
>
> The file that I am given to read by the the the plumed driver is .mdcrd
> file which was generated by amber itself. It is not a .molfile.
> And the issue here is that it could not read that .mdcrd file.
> &cntrl
> imin = 0,
>
> irest = 1,
> ntx = 5,
>
> nstlim = 1000000,
> dt = 0.002,
>
> ntt = 3,
> gamma_ln = 2.0,
> temp0 = 300,
> ig = -1,
>
> ntr = 0,
> ntc = 2,
> ntf = 2,
> nscm = 1000,
>
> ntb = 2,
> cut = 8.0,
>
> ntp = 1,
> taup = 2,
>
> ntpr = 5000,
> ntwx = 5000,
> ntwr = 5000,
>
> nmropt = 1,
> /
> I used the above structure to generate the .mdcrd file.
>
> When I give the input file plumed.dat in the input file of the MD
> simulation, it returns me the COLVAR file, which calculates the CV.
> But I want to analyse the trajectory after completing the full
> simulation. So I use the .mdcrd to calculate the collective variable,
> but the plumed driver have problem in reading the CRD file.
> And I also want to mention here that when I converted the .mdcrd file to
> .xtc file by mdconvert in mdtraj, the plumed driver worked with .xtc
> file but not with .mdcrd
>
>
>
>
> On 07-12-2023 20:55, Todd Minehardt wrote:
> > Munazzah,
> >
> > The issue starts with trying to read the trajectory file.
> >
> > It seems that your file type is molfile (.mol) - can you provide
> > details about what you used to generate the trajectory, as AMBER does
> > not write that format (that I'm aware of).
> >
> > Cheers,
> >
> > Todd
> >
> > On Thu, Dec 7, 2023 at 5:20 AM Munazzah Fatima Ansari via AMBER
> > <amber.ambermd.org> wrote:
> >
> >> 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
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Dec 08 2023 - 07:30:03 PST
