[gmx-users] Advice for simulating small DNA

[Joshua Ballanco]

On Feb 1, 2009, at 6:48 PM, Mark Abraham wrote:

> Joshua Ballanco wrote:
>> Hi,
>> I'm attempting to model a system involving a small DNA 3-mer.  
>> Without any explicit constraints, the helix begins to come apart  
>> around 0.75 ns to 1 ns into the simulation.
>
> Presumably you have a 3-mer of helices, of which at least one comes  
> apart. Does a single helix in water survive? (Giving a better  
> description of your simulation system would be a good idea!)

Apologies for not being more descriptive... It is a single strand of  
DNA containing 3 A-T base pairs. The system also contains a single  
Arginine residue. Simulating it in water leads to the single DNA  
strand gradually coming apart. With the DNA and water alone, the helix  
stays together much longer, but still eventually comes apart.

>> So I'm now attempting to add restraints for the base-pair H-bonds,  
>> but I'm having trouble. It seems like no matter what I try, my  
>> system reliably explodes within the first 1 ns. My constraints look  
>> like this:
>> [ distance_restraints ]
>> ; ai  aj  type  index type’ low up1 up2 fac
>> 18  136 1     0     2     0.0 2.0 2.1 1.0
>> 14  134 1     0     2     0.0 2.0 2.1 1.0
>> 43  114 1     0     2     0.0 2.0 2.1 1.0
>> 39  112 1     0     2     0.0 2.0 2.1 1.0
>> 68   92 1     0     2     0.0 2.0 2.1 1.0
>> 64   90 1     0     2     0.0 2.0 2.1 1.0
>> I've tried pre-equilibrating for up to 100 ps, but even that  
>> doesn't prevent the system from eventually exploding.
>
> Your .mdp settings for distance restraints may also be relevant here  
> - not least in setting the existence and magnitude of these  
> restraints.

As I understand, the only relevant lines are:

constraints         =  all-bonds
integrator          =  md
disre               =  simple

For PME I was using:

coulombtype         =  PME
rlist               =  0.55
rcoulomb            =  0.55
rvdw                =  0.55
fourierspacing      =  0.1375


>> 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