AMBER Archive (2009)

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

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Apr 13 2009 - 10:29:11 CDT

See section 5.2.4 of tutorial B1:
http://ambermd.org/tutorials/basic/tutorial1/section5.htm

> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf Of balaji nagarajan
> Sent: Monday, April 13, 2009 4:37 AM
> To: amber forumnew
> Subject: [AMBER] problem with explicit solvent in TMD
>
>
>
>
> Dear Amber !
>
>
>
>
>
>
>
>
>
>
> 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 .
>
>
>
> I have attached my input file , if i am
> doing some mistakes in flag
>
> let me know
>
>
>
>
>
>
>
> thanks in advance
>
> regards
>
> balaji
> UOM
>
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