Re: About restarting QM-MM simulation

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Wed Feb 13 2019 - 14:47:13 CST

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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