Dear all AMBER users,
I have a problem when I tried to use sander.LES (with amber8). Here are the
procedures I used it:
First, I minimized my non-LES system, and heated it up from 0K to 300K. Then
I used 'addles' to prepare the inputs for the LES. When I used 'addles', I
had the error about exceeding the compilation limit, and therefore I
modified the SIZE.h file and recompile addles. Then everything was OK when I
run 'addles' again. And this is the input for addles:
#######################################################
file rprm name=(LES_ini.prmtop) read
file rcvb name=(heat.rst) read
file wprm name=(LES.prmtop) wovr
file wcrd name=(LES.crd) wovr
action
omas
spac numc=1000 pick #mon 792 792 done
*EOD
######################################################
And I run molecular dynamics using LES, this is the input file (md1.in):
########################################################
LES_md1
&cntrl
imin = 0, irest = 1, ntx = 7,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0,
cut = 10, ntr = 0,
ntc = 2, ntf = 2,
tempi = 300.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0,
nstlim = 100000, dt = 0.001,
ntpr = 200, ntwx = 200, ntwr = 2000
/
##########################################################
And I run the job using:
$AMBERHOME/exe/sander.LES -O -i LES_md1.in -o LES_md1.out -p LES.prmtop -c
LES.crd -r LES_md1.rst -x LES_md1.mdcrd
And here is the output I got:
############################################################
-------------------------------------------------------
Amber 8 SANDER Scripps/UCSF 2004
-------------------------------------------------------
| Run on 01/18/2007 at 16:15:37
[-O]verwriting output
File Assignments:
| MDIN: LES_md1.in
| MDOUT: LES_md1.out
|INPCRD: LES.crd
| PARM: LES.prmtop
|RESTRT: LES_md1.rst
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: LES_md1.mdcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip
Here is the input file:
LES_md1
&cntrl
imin = 0, irest = 1, ntx = 7,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0,
cut = 10, ntr = 0,
ntc = 2, ntf = 2,
tempi = 300.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0,
nstlim = 100000, dt = 0.001,
ntpr = 200, ntwx = 200, ntwr = 2000
/
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags: MPI LES
getting new box info from bottom of inpcrd
| peek_ewald_inpcrd: Box info found
|Largest sphere to fit in unit cell has radius = 38.199
NATOM = 57536 NTYPES = 19 NBONH = 50378 MBONA = 6328
NTHETH = 13715 MTHETA = 8660 NPHIH = 25765 MPHIA = 16154
NHPARM = 0 NPARM = 1 NNB = 2124220 NRES = 15260
NBONA = 6328 NTHETA = 8660 NPHIA = 16154 NUMBND = 68
NUMANG = 142 NPTRA = 44 NATYP = 44 NPHB = 1
IFBOX = 1 NMXRS = 2000 IFCAP = 0 NEXTRA = 0
NCOPY = 1000
| Memory Use Allocated
| Real 4023896
| Hollerith 360478
| Integer 23531916
| Max Pairs 8285184
| Max Rstack 2199202
| Max Istack 287680
| Total 175435 kbytes
Exceeded MAXLES 57536
#########################################################################
Can anyone please tell me what is the problem here? it said " Exceeded
MAXLES 57536", where 57536 is the total atom number in the LES system.
Howeverm I have changed 'maxnatom=70000' in the SIZE.h file before I
recompile addles. Thank you for all your help in advance!
Best regards,
Kailee
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Received on Sun Jan 21 2007 - 06:07:23 PST
