Dear Matt,
This is just a rounding issue and the 0.02 will be scaled to zero by pmemd.
HTH
Ian
On 03/12/2014 06:00, "Matthew Harrigan" <harrigan.stanford.edu> wrote:
>Hi all,
>
>I've noticed that the total charge of a DMPC lipid (as computed by tleap)
>is not 0. I've created a pdb file with one DMPC lipid (see github gist
>link below), which I run through tleap as follows:
>
>source leaprc.lipid14
>source leaprc.ff14SB
>loadamberparams frcmod.ionsjc_tip3p
>mol = loadpdb dmpc.pdb
>
>charge mol
>>>> Total unperturbed charge: -0.000006
>>>> Total perturbed charge: -0.000006
>
>
>pdb file here:
>https://gist.github.com/mpharrigan/2b43a3bb5dcdb9bd2c94
>
>This may look like a rounding error, but it scales linearly in number of
>lipids. For a full size membrane system, it results in a noticeable
>charge; order 0.02e. Should I be worried about this? Why do these lipids
>appear to be charged?
>
>Thanks,
>Matt
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Received on Tue Dec 02 2014 - 23:00:02 PST
