AMBER Archive (2008)

Subject: AMBER: Problem in EVB and Trajectory analysis

From: sai kumar ramadugu (amberquestions_at_gmail.com)
Date: Fri Sep 05 2008 - 16:20:17 CDT

Dear Amber Users,
   can we do the trajectory analysis (imin = 5) with empirical valence
bond(EVB).

iam doing evb. after running the regular MD, i wanted to do the trajectory
analysis with imin = 5 , and ievb = 1, the output files of the two evb
states
have the energies only for the first frame, later the core is getting
dumped. the mdout file has the following lines in the end

                    FINAL RESULTS

   NSTEP ENERGY RMS GMAX NAME NUMBER
      1 1.6411E+02 1.9434E+01 1.1507E+02 C2 2012
 BOND = 681.3577 ANGLE = 995.9584 DIHED =
23.7634
 VDWAALS = -1523.0616 EEL = -39.5447 HBOND =
0.0000
 1-4 VDW = -5.9582 1-4 EEL = 31.5924 RESTRAINT =
0.0000
*| Closing evb_unit associated with file evbout*
minimization completed, ENE= 0.164107E+03 RMS= 0.194337E+02
minimizing coord set # 2
evb out file has

{NSTEP}: 0 {TIME}: 0.00000000
  [EVB MATRIX]
    164.10724812 1.00000000 1.00000000 164.37771410
error file has the following information

forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
libgm.so.0 00002AAAAAAB813E Unknown Unknown Unknown
sander.MPI 00000000008708FE Unknown Unknown Unknown
sander.MPI 000000000088A54C Unknown Unknown Unknown
sander.MPI 000000000088A8BB Unknown Unknown Unknown
sander.MPI 00000000008756A4 Unknown Unknown Unknown
sander.MPI 0000000000876D3A Unknown Unknown Unknown
sander.MPI 0000000000884794 Unknown Unknown Unknown
sander.MPI 000000000087E6C0 Unknown Unknown Unknown
sander.MPI 000000000086800F Unknown Unknown Unknown
sander.MPI 000000000073195E Unknown Unknown Unknown
sander.MPI 00000000004CCDA6 Unknown Unknown Unknown
sander.MPI 00000000004C0D76 Unknown Unknown Unknown
sander.MPI 00000000004BE6C8 Unknown Unknown Unknown
sander.MPI 00000000004B34D7 Unknown Unknown Unknown
sander.MPI 000000000040566A Unknown Unknown Unknown
libc.so.6 00000034EDE1D084 Unknown Unknown Unknown
sander.MPI 00000000004055A9 Unknown Unknown Unknown
0 - MPI_ALLGATHER : Invalid buffer pointer
[0] Aborting program !
[0] Aborting program!
forrtl: error (76): IOT trap signal
Any help is greatly appreciated
thanks in advance 

-- 
Sai K. Ramadugu

The Margulis Lab,
Dept of Chemistry,
Univ of Iowa

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