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 - 15:30:02 PST
