Hello,
You could also use iwrap=1. This will image the molecules inside the primary box during the simulation.
Miguel.
> Hello,
>
> You can put back the water using ptraj image. And you will see that all the water molecules will be inside the box again.
>
> JIten
> ----- Original Message -----
> From: Soon
> To: amber.scripps.edu
> Sent: Tuesday, June 01, 2004 6:08 PM
> Subject: AMBER: Periodic boundary simulation
>
>
> Hello all,
>
> I am using Amber8 and I made octahedron simulation box by
>
> xx=loadpdb xx.pdb
> Solvateoct xx TIP3PBOX 4
>
> on leap with ff03 paramters.
>
>
> After minimization of the water solvated system, I performed NVT molecular dynamics simulation to equilibrate the system for about 50.0 ps.
>
> Now, my question is why on earth the water molecules are coming out of the octahedron simulation box during this NVT molecular dynamics run ? As I know the water molecules are suppose to move around inside the simulation box during the MD simulation. Not out of the box.
> The system is not cluster system after all !
>
> Here is my MD input.
>
> test
> &cntrl
> ntb=1, ig=33333,
> tempi=300.0, temp0=300.0, ntt=1,
> irest=0, ntx=1,
> nstlim=40000,
> dt=0.0017, ntc=2, cut=9.0,
> ntwe=200, ntwx=200, ntpr=200,
> /
>
>
> Am I missing something ? Any comments will be appreciated. Thank you.
>
> Soon
>
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Received on Tue Jun 01 2004 - 12:53:00 PDT
