[gmx-users] (no subject)

[Justin A. Lemkul]

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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-- 
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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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