AMBER Archive (2009)

Subject: Re: [AMBER] problem with explicit solvent in TMD

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Apr 13 2009 - 06:41:41 CDT

yes, this comes up all the time so if you search on the amber web page for
ptraj and image I'm sure you'll find plenty of info to help you out.

>
>
> Dear Amber !
>
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> I am doing targeted molecular dynamics
> in explicit water
>
> I have two structures from the same
> sequence of DNA ,
>
> I have added TIP3P water to both the
> structures in truncated octahedron geometry . Minimized and
> equilibrated.,
>
> The number of molecules in both of them
> are equal , when the targeted molecular dynamics is
>
> given with periodic boundary condition
> , the water molecules are not bound together with the DNA, I have
> attached the picture with this ,
>
> I have seen the DNA tutorial , its
> possible to re image the trajectory with ptraj .
>
>
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> I have attached my input file , if i am
> doing some mistakes in flag
>
> let me know
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> thanks in advance
>
> regards
>
> balaji
> UOM
>
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