Molcas Forum

dkaliakin

Member

From: Northeastern University Boston

Registered: 2020-09-03

Posts: 7

QM/MM Molecular Dynamics with DFT

Dear Molcas Experts,

I am currently trying to run QM/MM molecular dynamics for ground singlet state with M062X density functional, but I am experiencing some issues with it.
Could you please suggest what could be a reason for the issue that I am describing below?

My input file is

>  COPY  $PATH/$Project.xyz  $WorkDir/$Project.xyz
>  COPY  $PATH/$Project.key  $WorkDir/$Project.key
>  EXPORT TINKER=/home/Molcas/tinker/bin

 &Gateway
Tinker
basis=aug-cc-pvdz
Group  =  Nosym
RICD

>> FOREACH ITER in (1 .. 500)

 &Seward
doanalytic

 &Espf
External  =  Tinker

 &SCF
KSDFT = M062X

&ALASKA

&Dynamix
 velver
 dt = 20
 velo = 1
 ther= 2
 temp = 300
 HOP=0

>>> EndDo

While my *.key file is

parameters /home/Molcas/tinker/params/oplsaa_mod.prm
QMMM 60
QM -1 36
MM -37 60
QMMM-MICROITERATION ON

The error that I get in the log file is

()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()

                                              &DYNAMIX

                                   only a single process is used
                       available to each process: 1.8 GB of memory, 1 thread
                                             pid: 35055
()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()

--- Stop Module: dynamix at Sun Sep 13 14:27:47 2020 /rc=_RC_INTERNAL_ERROR_ ---
*** files: QMMM.dyn.h5 xmldump
    saved to directory /scratch/d.kaliakin/14287912

>>> END FOREACH

.########################################################.
.# Some internal inconsistency of the code was detected #.
.########################################################.

While in *.err file I see the following message

HDF5-DIAG: Error detected in HDF5 (1.8.12) thread 0:
  #000: ../../src/H5F.c line 1585 in H5Fopen(): unable to open file
    major: File accessibilty
    minor: Unable to open file
  #001: ../../src/H5F.c line 1274 in H5F_open(): unable to open file: time = Sun Sep 13 14:27:47 2020
, name = '/scratch/d.kaliakin/14287912/QMMM/QMMM.rasscf.h5', tent_flags = 0

To me it appears that DYNAMIX module is trying to access *rasscf orbitals even despite the fact that I am using SCF module. However, I am not entirely sure if that is the main issue, or if something else is missing in my *key and *inp files. Could you please suggest how to address this issue and/or what am I missing in these calculations?

Thank you very much for your help.

niko

Member

From: Marseille

Registered: 2015-11-08

Posts: 59

Website

Re: QM/MM Molecular Dynamics with DFT

Hi,

It looks to be a dynamix related issue. Just to confirm my hypothesis, run the same calculation without calling the ESPF module. This will turn off QM/MM.

dkaliakin

Member

From: Northeastern University Boston

Registered: 2020-09-03

Posts: 7

Re: QM/MM Molecular Dynamics with DFT

Thank you very much for your quick response Nicolas. I just tried to run my calculations without the ESPF module, but I am still getting the same error as described above.

Last edited by dkaliakin (2020-09-14 21:21:20)