Sunil Thapa wrote:
Respectable Mark/Berk/David
I am trying to study diffusion of oxygen in water at a constant pressure
of 1 bar.
My system contains 2 oxygen molecules in 110 water molecules of the box
size 1.5 nm
I have set rvdw=0.7/0.5, rcoul=0.7/0.5 and rlist=0.7/0.5 in my main run
mdp file.
When I run the production run of 1 ns then I get an warning message as
follows and the run terminates. Please try to figure out what might have
been wrong.
Grid: 35 x 35 x 35 cells
WARNING: your box is exploding! (ncells = 42875)
Step Time Lambda
17200 34.40000 0.00000
Rel. Constraint Deviation: Max between atoms RMS
Before LINCS 1.000000 1 2 1.000000
After LINCS 1.000000 1 2 1.000000
Fatal error: Can not read/write topologies to file type unknown
If I change the LINCS to SHAKE with tau_p=0.5 it goes well but at the
last step it gives segmentation fault error. I checked the pdb after
energy minimization. The molecules are intact and the energy is well
converged.
If I increase tau_p=2.0, also at this step the error persists.
My system contains 2 oxygen molecules in 110 water molecules of the box
size 1.5 nm
I have set rvdw=0.7/0.5, rcoul=0.7/0.5 and rlist=0.7/0.5 in my main run
mdp file.
Can you post your complete .mdp file?
-Justin
Your help is a boon
Sunil
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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