AMBER: increasing the maximum value of NPHB parameter

From: Alena Shmygelska <oshmygel.cs.ubc.ca>
Date: 29 Nov 2004 21:05:08 -0800

Hello Amber Users:

I have the following problem, I'd like to increase the maximum value in
Amber 7 for:


NPHB from 200 -> to 3600 (affects ASOL, BSOL, HBCUT 200 -> 3600)

I tried to modify following sources:

1) parms.h
   
   (NPHB=3600) ASOL(3600), BSOL(3600)
   

2) changed the check on the value of NPHB in rdparm.f:

 if (numbnd.gt.5000 .or. numang.gt.900 .or. nptra.gt.1200 .or.
     $ nphb.gt.3600 .or. natyp.gt.60 .or. nttyp.gt.1830) then


but there must be some other place where I forgot to do the required
modification since currently sander MD produces a Segmentation fault
when running it with NTYPES = 37 NPHB = 561 (works fine when NTYPES = 37
(<60) NPHB < 200, nothing else has been changed except for value of
NPHB, that in turn changed sizes of ASOL, BSOL and HBCUT in prmtop).
Prmtop file seems to be parsed correctly in rdparm.f, the place where
segmentation fault occurs is: in sander.f right before it calls FASTWT.
Using a debugger I found that IX(I02) and IX(I14) do not refer to the
valid memory locations, IX array is declared of size I79. But since I
just started to familiarize myself with Fortran as well as I am not
familiar with all of the sander's module code, it's not obvious to me
what else should be changed to increase the size of NPHB parameter (may
be the size of common memory block?).

Appreciate all the help,
Thanks!
Alena

University of British Columbia,
Vancouver, Canada

Here is the output file:
--------------------------------------------------------------------------------
   1. RESOURCE USE:
--------------------------------------------------------------------------------

| Flags:
HAS_10_12
| NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation
| *** cutoff > system size, list only builds once
| INFO: Old style PARM file read

 NATOM = 37 NTYPES = 37 NBONH = 0 MBONA = 36
 NTHETH = 0 MTHETA = 35 NPHIH = 0 MPHIA = 34
 NHPARM = 0 NPARM = 0 NNB = 106 NRES = 37
 NBONA = 36 NTHETA = 35 NPHIA = 34 NUMBND = 36
 NUMANG = 35 NPTRA = 68 NATYP = 37 NPHB = 561
 IFBOX = 0 NMXRS = 1 IFCAP = 0 NEXTRA = 0


| Memory Use Allocated Used
| Real 2000000 5261
| Hollerith 400000 261
| Integer 2000000 818535

| Max Nonbonded Pairs: 5400000
 
| Duplicated 0 dihedrals
| Duplicated 34 dihedrals

--------------------------------------------------------------------------------
   2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------

TITLE

General flags:
     imin = 0, nmropt = 0

Nature and format of input:
     ntx = 1, irest = 0, ntrx = 1

Nature and format of output:
     ntxo = 1, ntpr = 400, ntrx = 1, ntwr
= 50
     iwrap = 0, ntwx = 400, ntwv = 0, ntwe
= 400
     ioutfm = 0, ntwprt = 0, idecomp = 0,
rbornstat= 0

Potential function:
     ntf = 1, ntb = 0, igb = 0, nsnb
= 99999
     ipol = 0, gbsa = 0
     dielc = 1.00000, cut =1000.00000, intdiel = 1.00000
     scnb =2.00000, scee = 1.20000

Frozen or restrained atoms:
     ibelly = 0, ntr = 0

Molecular dynamics:
     nstlim = 100000, nscm = 1000, nrespa = 1
     t = 0.00000, dt = 0.00100, vlimit = 20.00000

Temperature regulation:
     ig = 43919, ntt = 4, vrand = 0
     temp0 = 400.00000, tempi = 400.00000, heat = 0.00000
     dtemp = 25.00000, tautp = 0.20000

--------------------------------------------------------------------------------
   3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------

                                                                                
 begin time read from input coords = 0.000 ps

Program received signal SIGSEGV, Segmentation fault.
0x0807ba5b in fastwt_ ()
 





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Received on Tue Nov 30 2004 - 05:53:00 PST
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