[gmx-users] Parameter suggestion for locating an Iron atom between two carbon ring and preventing system blow up
Sajjad Kavyani
kavyani.sajjad at gmail.com
Sun Dec 25 15:54:51 CET 2016
Dear Mark,
That was my mistake not to mention that the EM/NVT/NPT was for the full
system (ferr+benz).
And also, with the -pforce 10000 in every NPT run, it was revealed that the
large forces were appeared on the ferrocene residue.
As in the EM step the maximum force cannot be taken to below zero values,
Is the ferrocene topology correct?
Is there a better way to keep ferrocene in the middle of the two rings?
Could you please take another look?
Regards
Sajjad
On Sun, Dec 25, 2016 at 11:46 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:
> 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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