[gmx-users] Advice for simulating small DNA

[Justin A. Lemkul]

Joshua Ballanco wrote:

<snip>

> For PME I was using:
> 
> coulombtype         =  PME
> rlist               =  0.55
> rcoulomb            =  0.55
> rvdw                =  0.55
> fourierspacing      =  0.1375

What force field are you using?  These cut-off's seem a bit bizarre for most of 
the standard force fields distributed with Gromacs.

-Justin

> 
> 
>>> If, however, I remove the distance restraints, the simulation has no 
>>> problem.
>>
>> Hmmm? This seems to contradict what you say above.
> 
> What I meant to say is that if I remove the line "disre = simple", then 
> the simulation has no problem (other than the helix coming apart). With 
> restraints, the system eventually explodes.
> 
> Thanks for taking a look!
> 
> Cheers,
> 
> Josh_______________________________________________
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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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