Hello Chris
So you mean to do a constrained MDS to let the lipids "fill the gaps"
between the box edges and lipids, after that do a unconstrained MDS,
then we'll get a fine structure, am I right?
Thank you very much, I'll try that
Xin Liu
On 9/7/06, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote:
If you can't write a script, then do the minimization and equilibration with
water frozen in the z dimension (freeze_groups = water; freeze_dim = n n y)
or
use constraints in the z dimension (posre.itp force constant 1000 along z
and 0
along x and y). This will stop it from going into the membrane. Before you
start, sort the initial PDB according to z (you could do this in excel),
remove
any waters that you don't want, resort according to original order, and run
pdb2gmx. Note that pope.pdb does have a small cluster of waters in the
membrane.
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