Hi,
I am trying to optimize the unit cell of YPO4·0.8H2O crystal structure using periodic boundary conditions with gaussian16. I am using pbepbe DFT method and LanL2DZ basis set. The calculations start, but when i check the structure in the generating .log file i can see that the atoms of the structure are displaced out of the box. Also, no convergence cycle starts. Instead, a warning appears saying that the total charge is not zero all the time, but it is practically zero:
[...]
-------------------- ATTENTION--------------------
Total charge is not ZERO --- 0.000000000085
-------------------- ATTENTION--------------------
ItDFit: ISolve= 4 NSavIt= 1000 ITol= 0 Tol= 1.00D-10 ItMax= 1519 IStorA=2
Conv0= 3.77D-09 BNorm= 7.05D+02 BPNorm= 2.96D+01
Conv= 1.00D-10 AccInt= 1.00D-12
Generalized Minimum Residual for N= 1419 ITol= 0 MaxL= 1000 KMP= 1000
Iter Natral Err Est Error Estimate
ISDGMR: 0 0.2616538D-03 0.2616538D-03
ISDGMR: 1 0.1900526D-03 0.1900526D-03
ISDGMR: 2 0.9030613D-04 0.9030613D-04
ISDGMR: 3 0.5787010D-04 0.5787010D-04
ISDGMR: 4 0.3491865D-04 0.3491865D-04
[...]
From this warning, the program starts to run cycles calculating the total charge always without success and repeating the same warning.Why do the atoms in the unit cell move outwards? What can I do to reduce the accuracy with which the program tries to estimate the initial charge?
Try to use larger cell parameters or cell boundaries. It seems like some of your molecule's atoms are at the edge or outside the cell at the entry step. This may help.
Gaussian is not the best software to perform Periodic Calculations
Try the new Amsterdam Modeling Suite. We could collaborate on this if you wish
https://www.sciencedirect.com/science/article/pii/S2210271X22001025
even after setting pbc in amber and increasing the box size, peptide still move out of the box slightly. how can i stop it from going out of the box
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