[gmx-users] Parameter suggestion for locating an Iron atom between two carbon ring and preventing system blow up
Mark Abraham
mark.j.abraham at gmail.com
Sun Dec 25 09:16:18 CET 2016
Hi,
What would you expect to happen to a large box with mostly vacuum when it
is coupled to a normal pressure? Should that be stable?
Mark
On Sun, 25 Dec 2016 09:18 Sajjad Kavyani <kavyani.sajjad at gmail.com> wrote:
> Dear experts,
>
> I'm trying to simulate a box of benzene with 25~35 ferrocene (C5H5-Fe-C5H5)
> in it.
> I have the benzene itp, but in the case of ferrocene I have a problem to
> choose suitable parameter.
> Each parameters I tried for ferrocene lead the system to blow up.
> EVEN in a empty box (6 6 6) with just 20 or 30 ferrocene (pure ferrocene)
> my system blows up in just 40000 steps (time step = 0.002)
> For pure ferrocene, energy minimization hardly reach forces below 1000 and
> just in the case of changing the Fe bonds from 1 to harmonic (type 6) I
> could manage to get below zero potential values. But again it hardly
> reaches below 1000!
> - The procedure before blowing up was:
> EM - NVT - NPT (in this step, blows up)
> EM - NVT (with posre) - NPT (with posre) - NPT (no posre && in this step.
> blows up)
> - For t/p coupling the 'berendsen' method was utilized. And constraints was
> set to 'none'.
> The following is the itp for ferrocene was used.
>
> Is it correct to define 10 bonds to keep Fe in the middle of the two rings?
> What should I do to prevent the blow up?
>
>
> This is atomtype.itp of Fe2+:
> [ atomtypes ]
>
> Fe2+ 6 55.84700 0.000 A 0.115816833358 0.0
>
> ######
> And, this is the ferrocene itp (OPLS ff):
>
>
> [ moleculetype ]
> ; molname nrexcl
> FRC 3
>
>
> [ atoms ]
> ;id type resnr residu a.name cgnr charge mass
> 1 opls_714 1 FRC CP1 1 -0.356 12.01100
> 2 opls_715 1 FRC HP1 2 0.156 1.00800
> 3 opls_714 1 FRC CP2 3 -0.356 12.01100
> 4 opls_715 1 FRC HP2 4 0.156 1.00800
> 5 opls_714 1 FRC CP3 5 -0.356 12.01100
> 6 opls_715 1 FRC HP3 6 0.156 1.00800
> 7 opls_714 1 FRC CP4 7 -0.356 12.01100
> 8 opls_715 1 FRC HP4 8 0.156 1.00800
> 9 opls_714 1 FRC CP5 9 -0.356 12.01100
> 10 opls_715 1 FRC HP5 10 0.156 1.00800
> 11 Fe2+ 1 FRC FeS 11 2.000 55.84700
> 12 opls_714 1 FRC CP6 12 -0.356 12.01100
> 13 opls_715 1 FRC HP6 13 0.156 1.00800
> 14 opls_714 1 FRC CP7 14 -0.356 12.01100
> 15 opls_715 1 FRC HP7 15 0.156 1.00800
> 16 opls_714 1 FRC CP8 16 -0.356 12.01100
> 17 opls_715 1 FRC HP8 17 0.156 1.00800
> 18 opls_714 1 FRC CP9 18 -0.356 12.01100
> 19 opls_715 1 FRC HP9 19 0.156 1.00800
> 20 opls_714 1 FRC CP0 20 -0.356 12.01100
> 21 opls_715 1 FRC HP0 21 0.156 1.00800
>
> [ bonds ]
> ; i j funct length force.c.
> ;;CyclPen1
> 1 2 1 0.105 307105.6
> 1 3 1 0.138 392459.2
> 3 4 1 0.105 307105.6
> 3 5 1 0.138 392459.2
> 5 6 1 0.105 307105.6
> 5 7 1 0.138 392459.2
> 7 8 1 0.105 307105.6
> 7 9 1 0.138 392459.2
> 9 10 1 0.105 307105.6
> 9 1 1 0.138 392459.2
> ;;CyclPen2
> 12 13 1 0.105 307105.6
> 12 14 1 0.138 392459.2
> 14 15 1 0.105 307105.6
> 14 16 1 0.138 392459.2
> 16 17 1 0.105 307105.6
> 16 18 1 0.138 392459.2
> 18 19 1 0.105 307105.6
> 18 20 1 0.138 392459.2
> 20 21 1 0.105 307105.6
> 20 12 1 0.138 392459.2
> ;;Iron with carbons:
> 11 1 6 0.202 300500
> 11 3 6 0.202 300500
> 11 5 6 0.202 300500
> 11 7 6 0.202 300500
> 11 9 6 0.202 300500
> 11 12 6 0.202 300500
> 11 14 6 0.202 300500
> 11 16 6 0.202 300500
> 11 18 6 0.202 300500
> 11 20 6 0.202 300500
>
> [ angles ]
> ; i j k funct angle force.c.
> ;;CyclPen1
> 1 3 5 2 108 10.0
> 3 5 7 2 108 10.0
> 5 7 9 2 108 10.0
> 7 9 1 2 108 10.0
> 9 1 3 2 108 10.0
> ;;CyclPen2
> 12 14 16 2 108 10.0
> 14 16 18 2 108 10.0
> 16 18 20 2 108 10.0
> 18 20 12 2 108 10.0
> 20 12 14 2 108 10.0
> --
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