From: M. A (matabay2010_at_gmail.com)
Date: Thu May 14 2020 - 05:39:54 CDT
---------- Forwarded message ---------
From: M. A <matabay2010_at_gmail.com>
Date: Tue, May 12, 2020 at 12:31 AM
Subject: Re: namd-l: FATAL ERROR: Charge placement error in QM-MM bond.
To: Mariano Spivak <marspivak_at_gmail.com>, NAMD <namd-l_at_ks.uiuc.edu>
first of all, I am very thankful. For annealing I can't say anything yet
because after just 3 steps I faced this error but during these 3 steps the
system was normal. but about your first reason, I think it can be correct.
As you mentioned (the numbering convention is different between NAMD and
VMD) atom 811 in pdb file should be atom 812 and this atom is QM atom (CA).
when I prepared my qm-input file I did it exactly like the tutorial and
(for QM region beta=1) and (for N-Terminal-direction: CA C occupancy= 1)
and for (C-terminal-direction C and O atoms will be removed from the QM
region and just C and CA occupancy= 1). So I think every thing is ok. but I
don't know the problem is because of what and how should I fix QM pdb file?!
also I increased cutoff or decreased step size
but it did'nt worked.
I will be more thankful if you check my files if you have any free time.
folder is attached.
On Mon, May 11, 2020 at 8:53 PM Mariano Spivak <marspivak_at_gmail.com> wrote:
> You can try increasing the cutoff value of your simulation, but I am
> pretty sure there is either an input problem or the annealing step just
> went wrong in a big way.
> Without any additional information, I would say the atom 811 is far away
> from the QM atoms, since it triggered the cutoff error, and that should
> mean atom 811 should not be bound to a QM atom.
> Load the system and trajectory into VMD and visualize the QM atoms and
> atom 811, CHECK the numbering convention is different between NAMD and VMD.
> If atom 811 is indeed far from the QM atoms, then you should fix the
> qm-input.pdb file.
> It is possible that during the annealing simulation the system behaved in
> a strange manner, i.e. system imploded, and that triggered the error. If
> that is the case, try a smoother annealing.
> On Mon, May 11, 2020 at 1:50 AM M. A <matabay2010_at_gmail.com> wrote:
>> Dear Mariano
>> As you know I could do my qmmm simulation. Minimization step was done
>> very well but in the Annealing part I faced this error:
>> ERROR: The MM atom 811 is bound to a QM atom, but it was not selected as
>> a poitn charge. Check your cutoff radius!
>> FATAL ERROR: Charge placement error in QM-MM bond.
>> [Partition 0][Node 0] End of program
>> I know this question is very simple for you but I'm not expert in DFT
>> that would be very kind of you if you help me for solving this problem.
>> best regards
>> Maryam Atabay
>> Ph.D in Nano Computational Chemistry
>> Department of Physics, Sharif University of Technology
-- Maryam Atabay Ph.D in Nano Computational Chemistry Department of Physics, Sharif University of Technology -- Maryam Atabay Ph.D in Nano Computational Chemistry Department of Physics, Sharif University of Technology
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