Re: [AMBER] QM/MM MD: Error reading box

From: emanuele falbo <>
Date: Mon, 25 May 2020 10:39:39 +0100

Thanks for the clarification. The box info in the topology was indeed
giving me
error during the MD. I have now changed it to the box lengths in the
and the dynamics now is going without issues so far.

Thanks for the support.


Il giorno dom 24 mag 2020 alle ore 14:27 David A Case <> ha scritto:

> On Sun, May 24, 2020, emanuele falbo wrote:
> >
> >Thanks for the heads-up. One more question. So, I looked up the box info
> >into the topology.prmtop:
> >
> >%FORMAT(5E16.8)
> > 9.00000000E+01 6.11010000E+01 5.99640000E+01 6.29031000E+01
> It is safest to use the box information that is in the restart file:
> that is what the program actually uses (it ignores what is in the prmtop
> file), and might be different from the prmtop values, if any NPT
> simulations have been performed.
> In your case, it sounds like what you did should be fine, but it's worth
> double checking.
> ...dac
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> AMBER mailing list

*Emanuele Falbo*
PhD student
Penfold group
School of Natural and Environmental Sciences
Bedson Building, Newcastle University
Newcastle upon Tyne, NE1 7RU
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Received on Mon May 25 2020 - 03:00:01 PDT
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