AMBER Archive (2004)

Subject: Re: AMBER: Periodic boundary simulation

From: darden (
Date: Tue Jun 01 2004 - 08:11:54 CDT

I might add that although the waters are not inside the cell, all relevant
interactions are imaged---that is, nonbond interactions are calculated
using the periodic images of the waters that are inside the cell---the
atoms are deliberately not wrapped back into the cell during the
simulation to facilitate analysis of motions
Tom Darden
 On Tue, 1 Jun 2004,
Soon wrote:

> 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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