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 - 11:53:00 PDT
