Actually I want to calculate Pair correlation function of all
Methane-Methane sites in water by taking methane concentration as 0.1M.
As parameters for methane is not defined in AMBER so i made a model of
methane which is as:
%VERSION VERSION_STAMP = V0001.000 DATE = 29/06/20 12:22:00
%FLAG TITLE
%FORMAT(20a4)
CH4
%FLAG POINTERS
%FORMAT(10I8)
5 2
%FLAG ATMTYP
%FORMAT(10I8)
1 2
%FLAG ATMNAME
%FORMAT(20a4)
C1 H1 H2 H3 H4
%FLAG MASS
%FORMAT(5e16.8)
1.20100000E+01 1.00800000E+00 1.00800000E+00 1.00800000E+00
1.00800000E+00
%FLAG CHG
%FORMAT(5e16.8)
-7.07754132E+00 1.76938533E+00 1.76938533E+00 1.76938533E+00
1.76938533E+00
%FLAG LJEPSILON
%FORMAT(5e16.8)
1.04308023E+06 9.71708117E+04 7.51607703E+03
%FLAG LJSIGMA
%FORMAT(5e16.8)
6.75612247E+02 1.26919150E+02 2.17257828E+01
%FLAG MULTI
%FORMAT(10I8)
1 4
%FLAG COORD
%FORMAT(5e16.8)
-0.23800000e+00 0.37300000e+00 0.00000000e+06 -0.23800000e+00
1.48600000e+00
0.00000000e+00 -1.28600000e+00 0.00200000e+00 -0.05700000e-00
0.33500000e+00
0.00200000e+00 -0.87900000e+00 0.23600000e+00 0.00200000e+00
0.93600000e+00
And the input file for this
-------------------------------------------------------------------------------------------------------------------------------------------
#!/bin/csh-f
cat > methane.inp <<EOF
&PARAMETERS
OUTLST='x''g', THEORY='DRISM', CLOSUR='KH',
!grid
NR=16384, DR=0.025, routup=384, toutup=0,
!MDIIS
NIS=20, DELVV=0.3, TOLVV=1.e-11,
!iter
KSAVE=-1, KSHOW=1, maxste=10000,
!ElStat
SMEAR=1, ADBCOR=0.5,
!bulk solvent properties
TEMPER=298, DIEps=78.497,
NSP=2
/
&SPECIES
DENSITY=55.5d0,
MODEL="/home3_jbod/rakesh_t/AMBER/amber16/dat/rism1d/model/SPC.mdl"
/
&SPECIES
DENSITY=0.1d0,
MODEL="/home3_jbod/rakesh_t/angad/methane.mdl"
/
EOF
rism1d methane > methane.out || goto error
-----------------------------------------------------------------------------------------------------------------------------------------------------------------
After this when I submit this input file for the methane-methane sites pair
correlation it does not converge ,it doesn't produce a result. here i am
showing some last lines of output file-
step=9992 Res= 2.6075188813231716E+03 MDIIS= 3
step=9993 Res= 2.6109946675001888E+03 MDIIS= 4
step=9994 Res= 4.8974676013859653E+03 MDIIS= 5
step=9995 Res= 3.5782908626505214E+05 MDIIS= 1
step=9996 Res= 2.6237492439706461E+03 MDIIS= 2
step=9997 Res= 2.6075188813231716E+03 MDIIS= 3
step=9998 Res= 2.6109946675001888E+03 MDIIS= 4
step=9999 Res= 4.8974676013859653E+03 MDIIS= 5
step=**** Res= 3.5782908626505214E+05 MDIIS= 1
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Received on Sat Jul 04 2020 - 05:30:04 PDT
