Re: About restarting QM-MM simulation

From: Marcelo C. R. Melo (melomcr_at_gmail.com)
Date: Wed Feb 13 2019 - 16:20:33 CST

Yes. When NAMD restarts and launches ORCA again (assuming you kept the same
qmBaseDir path **and contents*)*, ORCA will use the temporary files left
behind in the folder to start the following steps.

---
Marcelo Cardoso dos Reis Melo, PhD
Postdoctoral Research Associate
Luthey-Schulten Group
University of Illinois at Urbana-Champaign
crdsdsr2_at_illinois.edu
+1 (217) 244-5983
On Wed, 13 Feb 2019 at 14:47, Francesco Pietra <chiendarret_at_gmail.com>
wrote:
> Hi
>
>>  For QM/MM simulations to be properly managed by NAMD, your QM
>> calculation needs to "fit" inside MD steps.
>
>
> If this is the case, if I understand, by adding
>
> bincoordinates ./....restart.coor
> binvelocities  ./.....restart.vel
> extendedSystem ./....restart.xsc
>
> to NAMD config file, and restarting, ORCA takes the checkpoint from folder
> "/0". Or not?
>
> thanks
> francesco pietra
>
> On Wed, Feb 13, 2019 at 7:32 PM Marcelo C. R. Melo <melomcr_at_gmail.com>
> wrote:
>
>> Hi,
>> NAMD does not control ORCA in terms of pausing and resuming an SCF
>> calculation, so there is nothing in NAMD's config or restart file that
>> would inform ORCA of where it sopped, and how should it resume.
>> NAMD QM/MM can only be paused/resumed between MD steps, which is were you
>> will have "restart" files written. (In your case, given your "restartfreq",
>> every 100 MD steps). For QM/MM simulations to be properly managed by NAMD,
>> your QM calculation needs to "fit" inside MD steps.
>> Best,
>> Marcelo
>> ---
>> Marcelo Cardoso dos Reis Melo, PhD
>> Postdoctoral Research Associate
>> Luthey-Schulten Group
>> University of Illinois at Urbana-Champaign
>> crdsdsr2_at_illinois.edu
>> +1 (217) 244-5983
>>
>>
>> On Wed, 13 Feb 2019 at 09:34, Francesco Pietra <chiendarret_at_gmail.com>
>> wrote:
>>
>>> Hello
>>> How can NAMD-ORCA QM-MM simulations be correctly restarted? I mean in
>>> the context of namd.config in Example1 tutorial:
>>>
>>> structure       XXX_A1_box_ion.psf
>>>> coordinates     XXX_A1_box_ion.pdb
>>>>
>>>> # Output Parameters
>>>> binaryoutput    no
>>>> outputname      XXX_A1_out
>>>> outputenergies  1
>>>> outputtiming    1
>>>> outputpressure  1
>>>> binaryrestart   yes
>>>> dcdfile         XXX_A1_out.dcd
>>>> dcdfreq         1
>>>> XSTFreq         1
>>>> restartfreq     100
>>>> restartname     XXX_A1_out.restart
>>>
>>>
>>> In particular when no SCF convergence was not yet reached (in favorable
>>> cases, info says that SCF convergence is close to be reached), so that
>>> XXX_A1_out.restart was not provided.
>>>
>>> I was also unable to find on ORCA manual how to increase the number of
>>> SFC iterations above the default 125.
>>>
>>> Thanks for advice
>>> francesco pietra
>>> PS I understand that the ORCA calculation can be carried out separately
>>> but I have some reasons now to let NAM-ORCA working together.
>>>
>>

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