[gmx-users] Re: problem with simulation of phosphatidic acid, possibly in my topology?
himanshu khandelia
hkhandelia at gmail.com
Mon May 5 15:56:10 CEST 2008
PS: My previous email was accidentally sent from the gmail account of
my colleague, who uses the same workstation. My apologies. This is
just a disclaimer on her behalf.
On Mon, May 5, 2008 at 11:34 AM, himanshu khandelia
<hkhandelia at gmail.com> wrote:
> Hi,
>
> I am trying to run a simulation of a POPC bilayer mixed with some
> mono-anionic Phosphatidic acid (POPA) , where the choline group is
> replaced by a hydrogen atom. However, the energy of my simulation box
> diverges, and I am trying to fix the problem. I also tried running a
> simulation of PA solvated in water and a single sodium ion, but even
> that does not work. I will try to provide as much detail as possible,
> I hope someone can help point out some obvious error which I have not
> been able to debug over 3 days. In the simulation of a single PA
> molecule in water, MDRUN keeps complaining that the distance between
> atoms H1 and O4 is very high (> 4 nm or so). The problem probably lies
> in my topology, possibly in the bonded interactions?
>
> Thank you very very much for all suggestions.
>
> The headgroup of phosphatidic acid in my topology looks something like this:
>
> H1
> |
> (-) O4 O2
> \ /
> P3 (+)
> / \
> (-)O5 O6
> |
> C7-----etc..... (rest of lipid)
>
> The same region in the POPC topology looks something like this:
>
> C6-----etc (choline group)
> |
> (-) O9 O7
> \ /
> P8 (+)
> / \
> (-)O10 O11
> |
> C12---------etc .... (rest of lipid)
>
>
> Thus, only one new atom type, a H-atom was introduced. I replaced the
> C6 of POPC by H1 on POPA. O7, P8, O9 were replaced by O2, P3, O4 and
> so on (so atom indices differ by a factor of 5)
>
> In the following, I have copy-pasted the topology of POPA and POPC for
> the above regions. The topology for POPC is the one on Tieleman's
> webpage, of course. My topology is directly derived from it.
>
> ###############################################################################################
> ###### FOR POPA #######
> [ atoms ]
> ; nr type resnr residu atom cgnr charge mass
> 1 LHO 1 PAPA H1 1 0.400
> 1.0080 ; this is the new atom type, I defined it in the lipid.itp file
> and also described non-bonded interactions and pairtypes for this
> atom.
> 2 LOS 1 PAPA O2 1 -0.600 15.9994 ;
> 3 LP 1 PAPA P3 1 1.500 30.9738
> 4 LOM 1 PAPA O4 1 -0.800 15.9994
> 5 LOM 1 PAPA O5 1 -0.800 15.9994
> 6 LOS 1 PAPA O6 1 -0.700
> 15.9994 ; qtot:-1
> 7 LC2 1 PAPA C7 2 0.400 14.0270
>
> [bonds ]
> ; ai aj funct
> 1 2 1 0.10000E+00 0.31380E+06
> 2 3 1 0.16100E+00 0.25100E+06
> 3 4 1 0.14800E+00 0.37660E+06
> 3 5 1 0.14800E+00 0.37660E+06
> 3 6 1 0.16100E+00 0.25100E+06
> 6 7 1 0.14300E+00 0.25100E+06
> ....etc
> [ pairs ]
> ; ai aj funct
> 1 4 1
> 1 5 1
> 1 6 1
> 2 7 1
> 3 8 1
> 4 7 1
> .... etc ....
>
> [ angles ]
> ; ai aj ak funct
> 1 2 3 1 0.10960E+03 0.39750E+03
> 2 3 4 1 0.10960E+03 0.39750E+03
> 2 3 5 1 0.10960E+03 0.39750E+03
> 2 3 6 1 0.10300E+03 0.39750E+03
> 3 6 7 1 0.12000E+03 0.39750E+03
> 4 3 5 1 0.12000E+03 0.58580E+03
> 4 3 6 1 0.10960E+03 0.39750E+03
> 5 3 6 1 0.10960E+03 0.39750E+03
>
> [ dihedrals ]
> ; ai aj ak al funct phi0 cp mult
> 1 2 3 6 1 0.0 1.05 3
> 1 2 3 6 1 0.0 3.14 2
> 2 3 6 7 1 0.0 1.05 3
> 2 3 6 7 1 0.0 3.14 2
> #####################################################################################
>
> #####################################################################################
> ###### FOR POPC #######
>
> [ atoms ]
> ; nr type resnr residu atom cgnr charge mass
>
> ; 1 to 5 are from the choline group
>
> 6 LC2 1 POPC C6 1 0.4000
> 14.0270 ; qtot:1.0
> 7 LOS 1 POPC O7 1 -0.800
> 15.9994 ; qtot:0.54
> 8 LP 1 POPC P8 1 1.700
> 30.9738 ; qtot:2.3
> 9 LOM 1 POPC O9 1 -0.800
> 15.9994 ; qtot:1.5
> 10 LOM 1 POPC O10 1 -0.800
> 15.9994 ; qtot:0.7
> 11 LOS 1 POPC O11 1 -0.700 15.9994 ; qtot:0
> 12 LC2 1 POPC C12 2 0.400
> 14.0270 ; qtot:0.08
>
> [ bonds ]
> ; ai aj funct
> 6 7 1 0.14300E+00 0.25100E+06
> 7 8 1 0.16100E+00 0.25100E+06
> 8 9 1 0.14800E+00 0.37660E+06
> 8 10 1 0.14800E+00 0.37660E+06
> 8 11 1 0.16100E+00 0.25100E+06
> 11 12 1 0.14300E+00 0.25100E+06
>
> [ pairs ]
> ; ai aj funct
> 4 7 1
> 5 8 1
> 6 9 1
> 6 10 1
> 6 11 1
> 7 12 1
>
> [ angles ]
> ; ai aj ak funct
> 6 7 8 1 0.12000E+03 0.39750E+03
> 7 8 9 1 0.10960E+03 0.39750E+03
> 7 8 10 1 0.10960E+03 0.39750E+03
> 7 8 11 1 0.10300E+03 0.39750E+03
> 8 11 12 1 0.12000E+03 0.39750E+03
> 9 8 10 1 0.12000E+03 0.58580E+03
> 9 8 11 1 0.10960E+03 0.39750E+03
> 10 8 11 1 0.10960E+03 0.39750E+03
>
>
> [ dihedrals ]
> ; ai aj ak al funct phi0 cp mult
> 6 7 8 11 1 0.0 1.05 3
> 6 7 8 11 1 0.0 3.14 2
> 7 8 11 12 1 0.0 1.05 3
> 7 8 11 12 1 0.0 3.14 2
> ###############################################################################################
>
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