Assuming there is nothing wrong with your setup, sometimes you can help
DFTB converge by using a varialble in your QMMM namelist called telec or
something like that.
In the past, we have solved this issue using Telec = 200 or around that
I believe.
General good practice:
Never leave a run all day without looking at it, especially thew first
time you try something !
Adrian
On 2/20/23 8:09 AM, Maciej Spiegel via AMBER wrote:
> [External Email]
>
> Dear David,
>
> The QM region consists of 22 heavy atoms and 21 hydrogens.
>
> The job has been running all day and has produced a 1.2GB data file, which is nearly entirely filled with the given errors. I will do as you suggest.
>
> The `checkstructure` command:
>
>> parm protein.prmtop
>> trajin heat.rst
>> checkstructure
>> run
> was done on the heating (previous stage) coordinates and the output shows no errors, I assume...:
>
> ---------- RUN BEGIN -------------------------------------------------
>
> PARAMETER FILES (1 total):
> 0: BlaC.prmtop, 45184 atoms, 10568 res, box: Orthorhombic, 10304 mol, 10294 solvent
>
> INPUT TRAJECTORIES (1 total):
> 0: 'heat.rst' is a NetCDF AMBER restart file with coordinates, velocities, time, box, Parm BlaC.prmtop (Orthorhombic box) (reading 1 of 1)
> Coordinate processing will occur on 1 frames.
>
> BEGIN TRAJECTORY PROCESSING:
> .....................................................
> ACTION SETUP FOR PARM 'BlaC.prmtop' (1 actions):
> 0: [checkstructure]
> Using pair list.
> Total Grid memory: 240.592 MB
> TIME: Pair List Setup: 0.3338 s
> Grid dimensions: 53 55 57 (166155 total).
> Excluding bond interactions.
> Memory used by full exclusion list: 542.464 kB
> Mask [*] corresponds to 45184 atoms.
> Checking 45216 bonds.
> Imaging on.
> ----- heat.rst (1-1, 1) -----
> 100% Complete.
>
> Read 1 frames and processed 1 frames.
> TIME: Avg. throughput= 2.1715 frames / second.
>
> ACTION OUTPUT:
> TIME: Analyses took 0.0000 seconds.
>
> DATASETS (1 total):
> CHECK_00001 "CHECK_00001" (integer), size is 1 (0.004 kB)
> Total data set memory usage is at least 0.004 kB
>
> DATAFILES (1 total):
> STDOUT (Structure check)
>
> RUN TIMING:
> TIME: Init : 0.0000 s ( 0.01%)
> TIME: Trajectory Process : 0.4605 s ( 91.65%)
> TIME: Action Post : 0.0000 s ( 0.00%)
> TIME: Analysis : 0.0000 s ( 0.00%)
> TIME: Data File Write : 0.0000 s ( 0.01%)
> TIME: Other : 0.0419 s ( 0.08%)
> TIME: Run Total 0.5024 s
> ---------- RUN END ---------------------------------------------------
>
> Best,
> --
> Maciej Spiegel, MPharm
>
> Department of Pharmacognosy and Herbal Medicines
> Wroclaw Medical University
>
> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Ffarmaceut.github.io%2F&data=05%7C01%7Croitberg%40ufl.edu%7C5f2e4462db3647fcbd5108db1343cb1e%7C0d4da0f84a314d76ace60a62331e1b84%7C0%7C0%7C638124954117600621%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=QxjGFf3RU%2BFEt%2FkZ%2Bpr5uEYy2s6%2FvgnEhBw6bM4GWiA%3D&reserved=0 <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Ffarmaceut.github.io%2F&data=05%7C01%7Croitberg%40ufl.edu%7C5f2e4462db3647fcbd5108db1343cb1e%7C0d4da0f84a314d76ace60a62331e1b84%7C0%7C0%7C638124954117600621%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=QxjGFf3RU%2BFEt%2FkZ%2Bpr5uEYy2s6%2FvgnEhBw6bM4GWiA%3D&reserved=0>
> .ORCiD <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Forcid.org%2F0000-0002-8012-1026&data=05%7C01%7Croitberg%40ufl.edu%7C5f2e4462db3647fcbd5108db1343cb1e%7C0d4da0f84a314d76ace60a62331e1b84%7C0%7C0%7C638124954117600621%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=x%2B%2Fk7Fc11qQz2SycgdyoShspmSnJohLwQhf6h6IORaU%3D&reserved=0> @Publons <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpublons.com%2Fresearcher%2F4419515%2Fmaciej-spiegel%2F&data=05%7C01%7Croitberg%40ufl.edu%7C5f2e4462db3647fcbd5108db1343cb1e%7C0d4da0f84a314d76ace60a62331e1b84%7C0%7C0%7C638124954117600621%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=k5ycDLbAZpcK3EDpidWb4%2BXbKtluUmarRkTIXFcQcvk%3D&reserved=0>
>
> Reviewer at:
> Phytochemistry | Free Radical Research | Theoretical Chemistry Accounts
> Journal of Molecular Modeling | Frontiers in Bioscience-Landmark | Symmetry
>
>> Wiadomość napisana przez David A Case <david.case.rutgers.edu> w dniu 20.02.2023, o godz. 14:56:
>>
>> On Sun, Feb 19, 2023, Maciej Spiegel via AMBER wrote:
>>
>>> I run QM/MM computation but the QM region does not converge at all, and
>>> Amber keeps throwing errors:
>> How many atoms are in your QM region? Larger regions increase the chances
>> of SCF failures.
>>
>> Try running just enough steps to get to a failure, and look at the
>> coordinates in the restart file. See if the "checkstructure" action in
>> cpptraj reports any problems.
>>
>> ...good luck...dac
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=05%7C01%7Croitberg%40ufl.edu%7C5f2e4462db3647fcbd5108db1343cb1e%7C0d4da0f84a314d76ace60a62331e1b84%7C0%7C0%7C638124954117600621%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=JXrCwThjMDd%2BxPsVhbjtpE%2FEK%2Bpk%2FABWF%2BMYs1kTlpM%3D&reserved=0
--
Dr. Adrian E. Roitberg
V.T. and Louise Jackson Professor in Chemistry
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Feb 20 2023 - 07:00:02 PST
