[AMBER] Particles diffuse very far away from each other

From: ariana karakutuk <arianakarakutuk.hotmail.com>
Date: Tue, 28 Aug 2012 05:11:07 +0000

Hello all,
I'm new in AMBER and trying to learn more,I'm simulating an linear protein (120 residues) and I have 3 ions. I'm using GB method. I've done minimizing and heating (7 stages), but when I've tried to equilibrate it has sad:
I could not understand line 901:6835.5128068************-326.2661063************************************
*s in the inpcrd file often indicate an overflow of the Fortran format used to store coordinates in the inpcrd/restart files. This often happens when particles diffuse very far away from each other.
Here's my minimizing input file:&cntrl imin=1, maxcyc=1000, ncyc=500,cut=999., rgbmax=999., igb=1, ntb=0,ntpr=100/
Here's my heating input file:&cntrlimin=0, irest=0, ntx=1,nstlim=10000, dt=0.0005,ntc=2, ntf=2,ntt=1, tautp=1.0,tempi=0.0, temp0=50.0,ntb=0, igb=1,cut=999., rgbmax=999./
Here's my equilibration input file:&cntrlimin=0, irest=1, ntx=5,nstlim=500000, dt=0.002,ntc=2, ntf=2,ntt=1, tautp=0.5,tempi=325.0, temp0=325.0,ntpr=500, ntwx=500,ntb=0, igb=1,cut=999., rgbmax=999./
Thank you,Ariana
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Received on Mon Aug 27 2012 - 22:30:03 PDT
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