Is it possible they the separation is from periodic wrapping? Check the
image commands in cpptraj. Visualization might help to know if this is the
problem.
If not, perhaps your equilibration was too rapid or not well designed. See
Dan Roe's recent paper on equilibration for good protocols.
On Tue, Feb 15, 2022, 6:26 PM <b.ercig.nki.nl> wrote:
> Hello everyone,
>
>
>
> I am currently simulating a system which consists of 2 proteins and 1
> dsDNA in complex. I have made an production run of 10ns without any
> problems however, when I extend the simulation after 10ns, I see that the
> nucleotides in DNA strand is separating from the strand for some reason. I
> am not sure if I was able to explain the situation. But this did not seem
> to be a problem with starting structure to me, since the complex structure
> was intact during the minimization, heating etc…
>
>
>
> I used Amber FF14SB forcefield together with BSC1 forcefield.
>
>
>
> solvateBox com TIP3PBOX 10.0 (also tried octahedral box; did not work also)
>
>
>
> and I neutralize the system using Na+; Cl- ions.
>
>
>
> Below is the parameters being used in the production run:
>
> imin=0,irest=1,ntx=5,
>
> nstlim=5000000,dt=0.002,
>
> ntc=2,ntf=2,ig=-1,
>
> cut=8.0, ntb=2, ntp=1, taup=2.0,
>
> ntpr=500, ntwx=500, ntwr = 500, ioutfm=1,
>
> ntt=3, gamma_ln=2.0,
>
> temp0=300.0,
>
>
>
> Maybe I am missing something really obvious here, and I would be really
> happy to hear your feedbacks. Thanks all !
>
>
>
>
>
> Kind regards,
>
> Bogac Ercig
>
> Netherlands Cancer Institute
>
>
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Received on Tue Feb 15 2022 - 17:00:02 PST
