Hello,
I am doing ensemble refinement with PRE restraints using the fit.py script
file. My protein is hexamer with flexible tails. I found that during the
cooling steps, the VDW energy was very large and the time step is very small.
Following is an example.
*--- Dynamics ---- step= 300 ---- time= 0.021599 ---- delta_t=9.3514e-05 --*
| E(kin)+E(poten)= 31384.160 E(kin)= 576.838 temperature= 50.113 |
| E(poten)= 30807.3227460 grad= 34.6660233 ANGL= 5162.0899430 |
| BOND= 1152.4255825 IMPR= 1012.4482395 PRE= 2831.6677982 |
| RAMA=-21179.4077831 VDW= 41828.0989658
The starting structure was refined with no nonbonded violations and small VDW
energies as below.
*-- POWELL ------ step= 135 --- stepsize= 0.01000 --- energy evals= 44 -*
| E(poten)= -929.6124511 grad= 1.8164828 ANGL= 1041.7818070 |
| BOND= 226.5438108 IMPR= 137.7415772 RAMA= -3098.5804725 |
| VDW= 762.9008263 |
*------------------------------------------------------------------------------*
Is that possible that the VDW energy so high that the PRE energy can not be
refined?
Best wishes!
Yours,
Junhui Peng
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