Ok great, will do, thanks for your help!
Alan Dodd wrote:
Well, for the terminal methyl, you have no way of
knowing which way the hydrogeons are pointing... So
no. However, it is worth including the carbonyl
carbon (although it has no hydrogeons, so no order
parameter), as a reference point for
Well, for the terminal methyl, you have no way of
knowing which way the hydrogeons are pointing... So
no. However, it is worth including the carbonyl
carbon (although it has no hydrogeons, so no order
parameter), as a reference point for the next carbon
down.
--- Arneh Babakhani <[EMAIL PROTECTED
Hi Alan, great, thanks, I suspected something like that.
Then, is there a way to calculate the Scd order parameters for these
carbons, given that there are no explicit hydrogens???
Arneh
Alan Dodd wrote:
The first and last carbons are not calculated.
GROMACS needs to use a C-C bond on either
The first and last carbons are not calculated.
GROMACS needs to use a C-C bond on either side of each
carbon to place the hydrogens, and hence calculate the
order parameter.
--- Arneh Babakhani <[EMAIL PROTECTED]>
wrote:
> Hello,
>
> Now with the g_order bug fixed (see bugzilla #84) ,
> I'm try
Hello,
Now with the g_order bug fixed (see bugzilla #84) , I'm trying to
calculate the orderparameters for 13 carbon atoms of the the sn2 chain
(carbons 2B thru 2N) of a DMPC membrane. So I create an index file,
make a group for each type of carbon, then run g_order.
The groups in the inde
5 matches
Mail list logo
