[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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