Dear Jason,
Please find the attached files. I also attached the md1.out which contains
unfinished MD results.
Thank you.
Chinsu
On Thu, May 19, 2011 at 2:14 AM, Jason Swails <jason.swails.gmail.com>wrote:
> Can you attach your input files? This includes the topology file, inpcrd,
> and mdin. Segfaults are indicative of memory errors, but it's not at all
> specific.
>
> There may be something subtly wrong with your topology file, or it may be a
> bug.
>
> All the best,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
>
> On May 18, 2011, at 1:00 AM, Chinh Su Tran To <chinh.sutranto.gmail.com>
> wrote:
>
> > Dear Amber users,
> >
> > Again i got the same error of "segmentation fault" even whatever i
> modified
> > my batch-file. The "ndm_md1.rst" was not even created.
> >
> > I compared the "ndm_md1.out" with other successful runs (i.e other
> > "xx_md1.out"), i found that the process of running wat-md1.in was halted
> in
> > the first step, as shown below (this is extracted from the
> "ndm_md1.out"):
> >
> > *NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
> > 0.0
> > Etot = -64769.2683 EKtot = 0.0000 EPtot =
> > -64769.2683
> > BOND = 79.7941 ANGLE = 500.8945 DIHED =
> > 1498.9190
> > 1-4 NB = 453.3799 1-4 EEL = 7256.7348 VDWAALS =
> > 10279.1689
> > EELEC = -84838.1594 EHBOND = 0.0000 RESTRAINT =
> > 0.0000
> > Ewald error estimate: 0.8471E-04
> >
> ------------------------------------------------------------------------------
> > *
> >
> > Please help. I really have no idea what is going on. I think the
> > "ndm_md1.rst" had not been created because the process stopped
> unexpectedly.
> >
> > Thank you.
> > Chinsu
> >
> >
> >
> >
> > On Mon, May 16, 2011 at 7:46 PM, Chinh Su Tran To
> > <chinh.sutranto.gmail.com>wrote:
> >
> >> Dear Jason,
> >>
> >> This is my batch file:
> >>
> >> */usr/local/amber10/exe/sander -O -i ./file-in/wat-min1.in -o
> >> ./results/ndm_min1.out -p ./results/ndm-wat.prmtop -c
> >> ./results/ndm-wat.inpcrd -r ./results/ndm_min1.rst -ref
> >> ./results/ndm-wat.inpcrd
> >>
> >> /usr/local/amber10/exe/sander -O -i ./file-in/wat-min2.in -o
> >> ./results/ndm_min2.out -p ./results/ndm-wat.prmtop -c
> ./results/ndm_min1.rst
> >> -r ./results/ndm_min2.rst
> >>
> >>
> >> /usr/local/amber10/exe/sander -O -i ./file-in/wat-md1.in -o
> >> ./results/ndm_md1.out -p ./results/ndm-wat.prmtop -c
> ./results/ndm_min2.rst
> >> -r ./results/ndm_md1.rst -x ./results/ndm_md1.mdcrd -ref
> >> ./results/ndm_min2.rst
> >>
> >> /usr/local/amber10/exe/sander -O -i ./file-in/wat-md2.in -o
> >> ./results/ndm_md2.out -p ./results/ndm-wat.prmtop -c
> ./results/ndm_md1.rst
> >> -r ./results/ndm_md2.rst -x ./results/ndm_md2.mdcrd
> >>
> >> /usr/local/amber10/exe/ambpdb -p ./results/ndm-wat.prmtop <
> >> ./results/ndm_md2.rst > ./results/ndm_md2.pdb*
> >>
> >> And the part below is the error I got:
> >>
> >>
> >> **/var/spool/torque/mom_priv/*
> >> *jobs/5731.bircibm.SC <http://5731.bircibm.sc/>: line 17: 14885
> >>> Segmentation fault /usr/local/amber10/exe/sander -O -i ./file-in/
> >>> wat-md1.in -o ./results/ndm_md1.out -p ./results/ndm-wat.prmtop -c
> >>> ./results/ndm_min2.rst -r ./results/ndm_md1.rst -x
> >> ./results/ndm_md1.mdcrd
> >>> -ref ./results/ndm_min2.rst
> >>>
> >>> Unit 30 Error on OPEN:
> >>> ./results/ndm_md1.rst
> >>> /var/spool/torque/mom_priv/**jobs/5731.bircibm.SC<
> http://5731.bircibm.sc/>:
> >> line 25:
> >>> ./results/ndm_md2.rst: No such file or directory
> >>
> >> *
> >> I double-checked and found that the ndm_md1.rst was not created, causing
> >> the next command was not performed, so the second error led to "could
> not
> >> open the ndm_md2.rst"
> >>
> >> I viewed other threads from Amber archive titled "segmentation fault"
> >> saying about "molecular size", but i dont think this error was addressed
> >> because i ran the similar batch file for other larger molecules and they
> ran
> >> fine.
> >>
> >> Is it possible that it was related to the TIP3PBOX of solvent I used? I
> >> used TIP3PBOX 12 for this molecule.
> >>
> >> Thanks for your reply, and hope more help.
> >>
> >> Chinsu
> >>
> >>
> >> On Mon, May 16, 2011 at 7:27 PM, Jason Swails <jason.swails.gmail.com
> >wrote:
> >>
> >>> On Mon, May 16, 2011 at 6:42 AM, Chinh Su Tran To
> >>> <chinh.sutranto.gmail.com>wrote:
> >>>
> >>>> Dear Amber users,
> >>>>
> >>>> Below is the error I encountered when running a batch file of sander
> for
> >>> MD
> >>>> runs following 2-step minimization:
> >>>>
> >>>> */var/spool/torque/mom_priv/jobs/5731.bircibm.SC: line 17: 14885
> >>>> Segmentation fault /usr/local/amber10/exe/sander -O -i ./file-in/
> >>>> wat-md1.in -o ./results/ndm_md1.out -p ./results/ndm-wat.prmtop -c
> >>>> ./results/ndm_min2.rst -r ./results/ndm_md1.rst -x
> >>> ./results/ndm_md1.mdcrd
> >>>> -ref ./results/ndm_min2.rst
> >>>>
> >>>> Unit 30 Error on OPEN:
> >>>> ./results/ndm_md1.rst
> >>>> /var/spool/torque/mom_priv/jobs/5731.bircibm.SC: line 25:
> >>>> ./results/ndm_md2.rst: No such file or directory
> >>>> *
> >>>>
> >>>
> >>> I don't think you copied everything over correctly. Here it says that
> >>> ./results/ndm_md2.rst doesn't exist, but I don't see anywhere above
> where
> >>> you used that file.
> >>>
> >>>
> >>>> could anyone please give me a hint about this? I just dont understand
> >>> why
> >>>> it
> >>>> happened 'cause it ran fine for other molecules before. And why didnt
> it
> >>>> occur during minimization?
> >>>>
> >>>> Thank you very much, and really looking forward to your reply.
> >>>>
> >>>> Regards,
> >>>> Chinsu
> >>>>
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>>>
> >>>
> >>>
> >>> --
> >>> Jason M. Swails
> >>> Quantum Theory Project,
> >>> University of Florida
> >>> Ph.D. Candidate
> >>> 352-392-4032
> >>> _______________________________________________
> >>> 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
>
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Received on Wed May 18 2011 - 19:00:03 PDT
