I think methane.inp script is fine but there is some problem in methane.mdl
file.
One typo error in .mdl file is clearly visible in coordinates, i.e
0.00000000e+06 instead of 0.00000000e+00.
On Sat, Jul 4, 2020 at 5:53 PM angad sharma <angadsharma54.gmail.com> wrote:
> 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 Sun Jul 05 2020 - 11:30:03 PDT
