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-- 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 _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Wed May 18 2011 - 11:30:03 PDT