Dear Dan,
I ran this whole calculation in another machine which have 96GB of RAM and
24 core processors running in CENTOS6.
I created a input file which contains:
*trajin
/home/users/vijay/slot3/paper3-lyo-system-TRAJ-Only/onlyTraj-bcmLyo25perR/reImaged-bcmLyo25perR.nc
15001 15010hbond MyHB :1-128 out nhb.dat dist 3.5 angle 120 avgout
avghb.dat \ nointramol series solventacceptor :WAT.O solventdonor :WAT
\ solvout solvent_avg.dat bridgeout bridge.datrunwritedata solutehb.dat
MyHB[solutehb]writedata solventhb.dat MyHB[solventhb]lifetime
MyHB[solutehb] out solute.lifetime.datlifetime MyHB[solventhb] out
solvent.lifetime.datrunanalysis*
and I executed this file using cpptraj command:
*cpptraj topology -i hb-cpptraj2.in <
http://hb-cpptraj2.in>*
If you notice, I only choose 10 frames. and the calculation run fine. But
at the end it states as below:
* . . . . MyHB[solventhb]:12640 "BMR_121.O15-V"
(integer), size is 10 MyHB[solventhb]:8317 "BMR_80.O14-V" (integer),
size is 10 MyHB[solventhb]:8647 "BMR_83.O16-V" (integer), size is 10
MyHB[solventhb]:9574 "BMR_92.O25-V" (integer), size is 10
MyHB[solventhb]:964 "BMR_10.O25-V" (integer), size is 10
MyHB[solventhb]:3465 "BMR_34.O22-V" (integer), size is 10
MyHB[solventhb]:4531 "BMR_44.O26-V" (integer), size is 10
MyHB[solventhb]:3694 "BMR_36.O25-V" (integer), size is 10
MyHB[solventhb]:4324 "BMR_42.O25-V" (integer), size is 10DATAFILES:
nhb.dat (Standard Data File): MyHB[UU] MyHB[UV] MyHB[Bridge]
MyHB[ID]Segmentation fault (core dumped)*
I get three files avghb.dat, bridge.dat, *nhb.dat* and solvent_avg.dat. But
the nhb.dat file is empty. There is no data at all.
Other files contains data in their respective formats.
Why this happens and how to overcome?
Your help is much appreciated.
Thank you.
Vijay
On Thu, Feb 12, 2015 at 1:46 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Wed, Feb 11, 2015 at 6:32 PM, Vijay Achari <glycoamber.gmail.com>
> wrote:
> > Is this showing some error?
> >
> >
> >
> > DATAFILES:
> > nhb.dat (Standard Data File): MyHB[UU] MyHB[UV] MyHB[Bridge] MyHB[ID]
> > *** buffer overflow detected ***: cpptraj terminated
>
> Interesting - this indicates a memory issue. What version of cpptraj
> are you using (cpptraj --version)? What happens if you write out in
> grace format instead (change nhb.dat to nhb.avg)? The hbond time
> series command can be very memory hungry since you essentially need an
> array of size N (where N is the number of frames) for each hydrogen
> bond detected. What happens if you run without the 'series' keyword?
>
> -Dan
>
> > ======= Backtrace: =========
> > /lib/x86_64-linux-gnu/libc.so.6(+0x73f1f)[0x7f917d6fdf1f]
> > /lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x5c)[0x7f917d79582c]
> > /lib/x86_64-linux-gnu/libc.so.6(+0x10a6f0)[0x7f917d7946f0]
> > /lib/x86_64-linux-gnu/libc.so.6(+0x109bf9)[0x7f917d793bf9]
> > /lib/x86_64-linux-gnu/libc.so.6(_IO_default_xsputn+0xbc)[0x7f917d70629c]
> > /lib/x86_64-linux-gnu/libc.so.6(_IO_padn+0x6e)[0x7f917d6fa22e]
> > /lib/x86_64-linux-gnu/libc.so.6(_IO_vfprintf+0x2576)[0x7f917d6d6266]
> > /lib/x86_64-linux-gnu/libc.so.6(__vsprintf_chk+0x84)[0x7f917d793c84]
> > cpptraj[0x520100]
> > cpptraj[0x5335fb]
> > cpptraj[0x533ae2]
> > cpptraj[0x53655a]
> > cpptraj[0x526d93]
> > cpptraj[0x527aaf]
> > cpptraj[0x524a70]
> > cpptraj[0x516442]
> > cpptraj[0x51677b]
> > cpptraj[0x51e8f9]
> > cpptraj[0x51f3b5]
> > cpptraj[0x40a201]
> > /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5)[0x7f917d6abec5]
> > cpptraj[0x40a26b]
> > ======= Memory map: ========
> > 00400000-0071c000 r-xp 00000000 08:06 420960
> > /usr/local/apps/amber14/bin/cpptraj
> > 0091c000-00969000 r--p 0031c000 08:06 420960
> > /usr/local/apps/amber14/bin/cpptraj
> > 00969000-00971000 rw-p 00369000 08:06 420960
> > /usr/local/apps/amber14/bin/cpptraj
> > 00971000-0098a000 rw-p 00000000 00:00 0
> > 02924000-107b1000 rw-p 00000000 00:00 0
> > [heap]
> > 7f917cb4c000-7f917d00d000 rw-p 00000000 00:00 0
> > 7f917d44e000-7f917d489000 r-xp 00000000 08:06 272697
> > /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
> > 7f917d489000-7f917d688000 ---p 0003b000 08:06 272697
> > /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
> > 7f917d688000-7f917d689000 r--p 0003a000 08:06 272697
> > /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
> > 7f917d689000-7f917d68a000 rw-p 0003b000 08:06 272697
> > /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
> > 7f917d68a000-7f917d845000 r-xp 00000000 08:06 683092
> > /lib/x86_64-linux-gnu/libc-2.19.so
> > 7f917d845000-7f917da45000 ---p 001bb000 08:06 683092
> > /lib/x86_64-linux-gnu/libc-2.19.so
> > 7f917da45000-7f917da49000 r--p 001bb000 08:06 683092
> > /lib/x86_64-linux-gnu/libc-2.19.so
> > 7f917da49000-7f917da4b000 rw-p 001bf000 08:06 683092
> > /lib/x86_64-linux-gnu/libc-2.19.so
> > 7f917da4b000-7f917da50000 rw-p 00000000 00:00 0
> > 7f917da50000-7f917da66000 r-xp 00000000 08:06 659472
> > /lib/x86_64-linux-gnu/libgcc_s.so.1
> > 7f917da66000-7f917dc65000 ---p 00016000 08:06 659472
> > /lib/x86_64-linux-gnu/libgcc_s.so.1
> > 7f917dc65000-7f917dc66000 rw-p 00015000 08:06 659472
> > /lib/x86_64-linux-gnu/libgcc_s.so.1
> > 7f917dc66000-7f917dd6b000 r-xp 00000000 08:06 683111
> > /lib/x86_64-linux-gnu/libm-2.19.so
> > 7f917dd6b000-7f917df6a000 ---p 00105000 08:06 683111
> > /lib/x86_64-linux-gnu/libm-2.19.so
> > 7f917df6a000-7f917df6b000 r--p 00104000 08:06 683111
> > /lib/x86_64-linux-gnu/libm-2.19.so
> > 7f917df6b000-7f917df6c000 rw-p 00105000 08:06 683111
> > /lib/x86_64-linux-gnu/libm-2.19.so./hb-Analysis.cpptraj: line 39: 2888
> > Aborted (core dumped) cpptraj $top <<EOF
> >
> >
> > trajin $trajpath/reImaged-$system.nc 15001 20000
> >
> >
> > # COMMAND
> >
> > hbond MyHB :1-128 out nhb.dat dist 3.5 angle 120 avgout avghb.dat
> > nointramol series solventacceptor :WAT.O solventdonor :WAT solvout
> > solvent_avg.dat bridgeout bridge.dat
> > run
> > writedata solutehb.dat MyHB[solutehb]
> > writedata solventhb.dat MyHB[solventhb]
> > lifetime MyHB[solutehb] out solute.lifetime.dat
> > lifetime MyHB[solventhb] out solvent.lifetime.dat
> > runanalysis
> >
> >
> > EOF
> >
> >
> >
> >
> > Thank you
> > Vijay
> >
> > On Thu, Feb 12, 2015 at 2:21 AM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> >
> >> Hi,
> >>
> >> On Wed, Feb 11, 2015 at 10:35 AM, Vijay Achari <glycoamber.gmail.com>
> >> wrote:
> >> > So far I tried to execute a command as shown below:
> >> >
> >> > *hbond :1-128 out nhb.dat dist 3.5 angle 120 avgout avghb.dat
> nointramol
> >> > series*
> >> >
> >> > But I dont know what are the additional options I need to add in
> order to
> >> > calculate the solute-solvent (lipid-water) hydrogen bonding. And
> continue
> >> > with lifetime analysis, although you have mentioned about lifetime
> >> > calculation in your earlier email.
> >>
> >> You will need to use the 'solventdonor' and 'solventacceptor'
> >> keywords. I also recommend giving your hydrogen bond data set a name
> >> to make it easier to refer to when writing out and analyzing your time
> >> series data. So you may want to modify your input like so:
> >>
> >> hbond MyHB :1-128 out nhb.dat dist 3.5 angle 120 avgout avghb.dat \
> >> nointramol series solventacceptor :WAT.O solventdonor :WAT \
> >> solvout solvent_avg.dat bridgeout bridge.dat
> >> run
> >> writedata solutehb.dat MyHB[solutehb]
> >> writedata solventhb.dat MyHB[solventhb]
> >> lifetime MyHB[solutehb] out solute.lifetime.dat
> >> lifetime MyHB[solventhb] out solvent.lifetime.dat
> >> runanalysis
> >>
> >> The manual should definitely contain better examples, but it still has
> >> some useful information. I highly recommend going over the manual
> >> entries for the 'hbond' and 'lifetime' commands just to make sure you
> >> understand what each keyword is doing. Hope that this helps, let me
> >> know if you have any more questions.
> >>
> >> -Dan
> >>
> >> >
> >> > Could you kindly help me here?
> >> > Appreciate your help in advance.
> >> >
> >> > Thanks
> >> > Vijay
> >> >
> >> >
> >> > On Thu, Feb 12, 2015 at 12:44 AM, Daniel Roe <daniel.r.roe.gmail.com>
> >> wrote:
> >> >
> >> >> Hi,
> >> >>
> >> >> On Wed, Feb 11, 2015 at 3:18 AM, Vijay Achari <glycoamber.gmail.com>
> >> >> wrote:
> >> >> > I don't understand the meaning of <*dsetarg0*> file. despite it is
> >> saying
> >> >> > about data file. But which data file and how to obtain this file?
> >> >>
> >> >> As stated in the manual, this argument pertains to data sets:
> >> >>
> >> >> <dsetarg0> [<dsetarg1> ...] Argument(s) specifying datasets to be
> used.
> >> >>
> >> >> The data sets can be data that have been generated by cpptraj during
> a
> >> >> run, or previously read in with the 'readdata' command. For example,
> >> >> say you have a data file named solventlifetime.dat which contains
> >> >> hydrogen bond time series data (from 'hbond series') in columns,
> e.g.:
> >> >>
> >> >> #Frame DC5_1.N3-V DC5_1.O2-V
> >> >> 1 1.0000 1.0000
> >> >> 2 0.0000 1.0000
> >> >> ...
> >> >>
> >> >> You can read the data in and perform lifetime analysis (over windows
> >> >> of size 5000) using the following input:
> >> >>
> >> >> readdata solventlifetime.dat
> >> >> runanalysis lifetime out life.gnu solventlifetime.dat window 5000
> >> >>
> >> >> Note that since I didn't provide a data set name to the 'readdata'
> >> >> command (via 'name <set name>'), the file name is chosen as default.
> >> >> You can see what data sets are currently loaded with 'list dataset'.
> >> >>
> >> >> Note that the hydrogen bond time series data is not written out
> >> >> automatically - you need to save it using a 'writedata' command after
> >> >> 'hbond' is run, like so:
> >> >>
> >> >> parm ../DPDP.parm7
> >> >> trajin ../DPDP.nc
> >> >> hbond HB out hbond.dat .N,H,C,O series avgout hbavg.dat printatomnum
> >> >> run
> >> >> write solutehb.agr HB[solutehb]
> >> >> runanalysis lifetime HB[solutehb] out lifehb.gnu window 10
> >> >>
> >> >> There are two things to note in the above input. The first is that I
> >> >> am issuing a 'run' command before writing or performing analysis on
> >> >> the hydrogen bond time series data. This is because unlike some other
> >> >> commands (like e.g. 'distance'), cpptraj doesn't know if any data (in
> >> >> this case hydrogen bonds) is actually present in the system until the
> >> >> analysis is actually run. The second is that I'm using a data set
> >> >> aspect (in this case [solutehb]) to select only solute-solute
> hydrogen
> >> >> bonds.
> >> >>
> >> >> This should be explained better in the manual, and there is a
> tutorial
> >> >> in the works, but for now I recommend you read section 28.3 of the
> >> >> Amber 14 manual (Data Sets and Data Files), and maybe run through the
> >> >> two existing cpptraj tutorials
> >> >> (http://ambermd.org/tutorials/#analysis) to become more familiar
> with
> >> >> data sets etc in cpptraj.
> >> >>
> >> >> Hope this helps - let me know if you have any more questions,
> >> >>
> >> >> -Dan
> >> >>
> >> >>
> >> >> >
> >> >> > Anyway I tried something like below:
> >> >> >
> >> >> >
> >> >> >
> >> >> > cpptraj topology << EOF
> >> >> >
> >> >> > *lifetime out hb-LifeTime-bcmLyo25perR.out
> >> >> > HB_inBothLayer_001_128-bcmLyo25perR.tbl cut 0.5 greater*
> >> >> >
> >> >> > EOF
> >> >> >
> >> >> >
> >> >> >
> >> >> >
> >> >> > with *HB_inBothLayer_001_128-bcmLyo25perR.tbl * is the output file
> of
> >> >> > hydrogen bonding.
> >> >> >
> >> >> > But this fail to run.
> >> >> > I wish to get some here.
> >> >> >
> >> >> > Regards
> >> >> > Vijay
> >> >> > _______________________________________________
> >> >> > AMBER mailing list
> >> >> > AMBER.ambermd.org
> >> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >>
> >> >>
> >> >>
> >> >> --
> >> >> -------------------------
> >> >> Daniel R. Roe, PhD
> >> >> Department of Medicinal Chemistry
> >> >> University of Utah
> >> >> 30 South 2000 East, Room 307
> >> >> Salt Lake City, UT 84112-5820
> >> >> http://home.chpc.utah.edu/~cheatham/
> >> >> (801) 587-9652
> >> >> (801) 585-6208 (Fax)
> >> >>
> >> >> _______________________________________________
> >> >> AMBER mailing list
> >> >> AMBER.ambermd.org
> >> >> http://lists.ambermd.org/mailman/listinfo/amber
> >> >>
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >>
> >> --
> >> -------------------------
> >> Daniel R. Roe, PhD
> >> Department of Medicinal Chemistry
> >> University of Utah
> >> 30 South 2000 East, Room 307
> >> Salt Lake City, UT 84112-5820
> >> http://home.chpc.utah.edu/~cheatham/
> >> (801) 587-9652
> >> (801) 585-6208 (Fax)
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Feb 12 2015 - 01:30:03 PST
