On Thu, Jan 17, 2013, DEBOSTUTI GHOSHDASTIDAR wrote:
>
> I am simulating DNA in a solvent. After thorough minimization, I
> heated up the system to 298K keeping the DNA restrained and thereafter
> performed NPT at 298K keeping the restraints on. However, the system
> showed a SHAKE error saying "SHAKE cannot be accomplished". So I read
> out the last few frames just before the error and using VMD saw that a
> C-H bond of one molecule of the solvent is stretched too much. When I
> repeated the simulation, the error occured again, this time for a
> different solent molecule and a N-H bond. During this entire procedure
> i was using dt=0.002.
I doubt that very many people have experience with simulation of DNA in
solvents other than water. There may be large forces on the solvent
molecules, and it is certainly possible that there are problems with whatever
force field parameters you are using for the solvent. Or, you may still need
to equilibrate for longer (you don't say how long the equilibration was...)
It's not too uncommon to need to use dt=0.001 for the first stages of a
simulation.
>
> Here's my input for md
> &cntrl
> imin = 0, ntx = 7, irest = 1,
> ntpr = 1000, ntwx = 1000, ntwe = 0,
> ntc = 2, ntf = 2,iwrap = 1,nstlim = 500000, dt =0.002,
> tempi=298.0, temp0 = 298.0, ntt =1, tautp =2.0,
> cut = 15.0, ntb = 2,ntp = 1,taup = 2.0,pres0 = 1.0
^^^^^^^^^^^^
This is way too big....consider using a value in the range of 8-10 Ang.
...dac
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Received on Thu Jan 17 2013 - 06:30:03 PST
