AMBER Archive (2008)

Subject: AMBER: problem with minimization

From: luzhenw1_at_msu.edu
Date: Thu Aug 07 2008 - 10:13:17 CDT

Dear all:

         I have a problem when try to do energy
minimization of an average structure of MD trajectory.
Here is the error message:

 forrtl: severe (174): SIGSEGV, segmentation fault
occurred
forrtl: severe (174): SIGSEGV, segmentation fault
occurred
rank 1 in job 23  msunmr6_33508   caused collective
abort of all ranks
  exit status of rank 1: return code 174

for the output, it stops at the first step:

    NSTEP       ENERGY          RMS           
GMAX         NAME    NUMBER
      1     NaN            NaN             
8.1543E+17     HD22     3787

 BOND    =   461855.0703  ANGLE   =   197335.8187 
DIHED      =     8488.8753
 VDWAALS =  NaN           EEL     =  NaN          
HBOND      =        0.0000
 1-4 VDW = *************  1-4 EEL =    25910.9799 
RESTRAINT  =        0.0000

the input file is simple: 

&cntrl
     imin=1, maxcyc=2500,
     ncyc=1000, ntb=0,
     ntr=0,
    cut=12,
   
  
     I tried both gas phase and explicit solvent model
and failed. the result shown here is for gas phase. 

     it is noticed  that the average structure have
some clash due to average. I think this might have
something to do with the error.  However, I don't know
how to deal with it and finish the minimization. Any
suggestions are welcome. Thanks in advance. please let
me know if further information is necessary for you. 

 

         

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