Hi,
First, when you analyze the stripped trajectory are you using a
matching "stripped" topology file?
Also, this is the second ptraj input you list:
On Sat, Feb 12, 2011 at 3:41 AM, bharat lakhani <lakhbharat.gmail.com> wrote:
> trajin X3_md.1.trj 1 500 10
> trajin X3_md.2.trj 1 500 10
> trajin X3_md.3.trj 1 500 10
> trajin X3_md.4.trj 1 500 10
> [....etc]
>
> strip :WAT
Just to make certain does the [....etc] part of this input include the
'image' and 'center' commands? If so, try leaving out the
image/centering of the second strand, i.e. just use:
center :1-12 origin mass
image origin center familiar
center :1-24 origin mass
image origin center familiar
and see if that improves things.
-Dan
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Received on Sat Feb 12 2011 - 07:00:02 PST
