[AMBER] iwrap=1 issue

From: Hirdesh Kumar <hirdesh.iitd.gmail.com>
Date: Mon, 2 May 2016 13:57:07 +0200

I did all atom simulation of my protein-ligand complex on 2 GPUs (Tesla
M2090). Here is my input file:

 All atom simulation
 &cntrl
 imin = 0,
 irest = 1,
 ntx = 5,
 ntb = 2,
 ntp = 1,
 cut = 8.0,
 ntc = 2,
 ntf = 2,
 tempi = 298.0,
 temp0 = 298.0,
 ntt = 3,
 taup = 2,
 ig = 47123,
 iwrap = 1,
 gamma_ln = 1.0,
 nstlim = 35000000, dt = 0.002
 ntpr = 1000, ntwx = 1000, ntwr = 50000
 &end


After 13399000 steps, simulation stopped and I got following error in
output file:

"Unit 16 Error on OPEN: prod3.rst"

When I generated the pdb file using ambpdb, I observed that proteins are
ligands are outside the water-box (see attached image).

Can anyone suggest me what am I doing wrong.





*​Thanks,Hirdesh​*


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Received on Mon May 02 2016 - 05:00:05 PDT
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