Hi Amber Developers/ Users,
I am performing NEB, moving the system from its "Open" structure to the
"Close" structure. This comprises of large conformational transition.
I had minimised the initial and final structures until convergence before
starting NEB.
I have played around with spring constants ( skmin/skmax ranging from 0.5
to 50 at various stages), temperatures (slow to fast heating & slow
cooling) and the number of images to represent this transition (I performed
TMD to sample images from open to close transition. Used conformations from
TMD to represent the number of images I supply NEB to start with - I used 8
- 64 images to represent transition with just 2 to 32 conformations from
TMD).
I performed implicit solvent NEB in 6 stages:
1HEAT - spring constant
ranging from 0.5 - 10 for 40ps of MD with a 0.5fs time step raising temp
from 0 to 300K
2ANNEAL - spring constant
ranging from 1 - 50 for 1ns of MD with a 1fs time step raising temp from
300 to 500K
3EQUIL - spring constant
ranging from 1 - 50 for 2ns of MD with a 2fs time step equilibrating at 500K
4COOL - spring constant
ranging from 1 - 50 for 2ns of MD with a 2fs time step decreasing temp from
500 to 300K
5EQUIL - spring constant
ranging from 1 - 50 for 2ns of MD with a 2fs time step equilibrating at 300K
6COOL - spring constant
ranging from 1 - 50 for 2ns of MD with a 2fs time step decreasing temp from
300 to 0K
6EQUIL - spring constant
ranging from 1 - 50 for 2ns of MD with a 2fs time step equilibrating at 0K
**spring constant ranging from x - y: is across different attempts not in a
single simulation.
I am having the following issues:
1) Irrespective of the values I play around with, NEB constantly
imposes a barrier height. This leads to the unfolding of the helix in the
region I try to perform the tgtrmsmask in.
2) At the images Where the conformational transition is sampled, the
energies go very high and the potential energy gets to NaN (This mostly
happens due to the helix unfolding raising dihedral and vdw energies to
shoot up).
3) Even though I used 32 evenly spaced conformers (sampling the
transition) from TMD to sample 64 images in NEB, the transition is not
smooth, with a sudden drop in energy for the last but one conformer. This
drop in energy moves towards the left as I decrease the number of
conformers I use to represent transition. For eg: If I just use open and
closed conformers (as in the tutorial), the dip in the energy is in the
centre image. As I increase the Conformers from TMD the dip move towards
the right from the centre. To negate this I tried an unequal number of
images used to represent transition: the first 4 images were sampled from
"Open" and the rest from "Close", and so on and so forth.
Any help is appreciated !!!
Regards,
Aravind R
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Received on Thu Oct 20 2022 - 23:30:03 PDT
