Hi Angad,
I’ll also point out that your values for LJEPSILON and LJSIGMA are enormous. I recommend reading the descriptions in section 7.8.1 (p. 135) of the Amber 20 manual. You can also see examples in $AMBERHOME/dat/rism1d/mdl. These use common models so you can compare published parameters against what is in the MDL files.
Hope this helps,
Tyler
> On Jul 5, 2020, at 11:05 AM, Leena Aggarwal <leena.hrc.gmail.com> wrote:
>
> 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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>>
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Received on Sun Jul 05 2020 - 15:30:04 PDT
