Which version of Amber?
-----Original Message-----
From: Matthew Guberman-Pfeffer via AMBER <amber.ambermd.org>
Sent: Sunday, November 20, 2022 2:38 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] Vacuum simulation problem
Dear AMBER community,
I’m really puzzled by a segmentation fault error I’m getting for simply trying to do a vacuum minimization. Below is my input file and command. Note that it works fine with SANDER, but crashes with PMEMD. No error message is printed by PMEMD to the end of the out file (see below for output).
Input:
&cntrl
ig=-1,
imin=1, ntmin=2, ncyc=1000, maxcyc=1000,
ntb=0, igb=0, cut=9999,
ntc=2, ntf=1,
ntr=0, nmropt=0,
ntwr=100, ntwx=100, ntpr=100,
ntxo=2, ioutfm=1,
/
pmemd -O -i min.in -p BeforeState_vac.parm7 -c BeforeState_vac.rst7 -o min.out -r min.rst7 -inf min.info
Output to terminal:
Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
Backtrace for this error:
#0 0x2b2ae3e583ff in ???
#1 0x48b3ee in ???
#2 0x4ab713 in ???
#3 0x4dbea6 in ???
#4 0x50a113 in ???
#5 0x42403c in ???
#6 0x2b2ae3e44554 in ???
#7 0x42406c in ???
#8 0xffffffffffffffff in ???
Segmentation fault
End of output file:
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
NATOM = 53 NTYPES = 10 NBONH = 26 MBONA = 27
NTHETH = 55 MTHETA = 36 NPHIH = 113 MPHIA = 94
NHPARM = 0 NPARM = 0 NNB = 266 NRES = 5
NBONA = 27 NTHETA = 36 NPHIA = 94 NUMBND = 17
NUMANG = 31 NPTRA = 33 NATYP = 12 NPHB = 0
IFBOX = 0 NMXRS = 21 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Coordinate Index Table dimensions: 0 0 0
What is going wrong? What should I check?
Best,
Matthew
88,1 Bot
_______________________________________________
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
Received on Sun Nov 20 2022 - 14:00:02 PST
