[AMBER] Sander bomb: how to create a larger box

From: Ruth Helena Tichauer <rhtichau.laas.fr>
Date: Thu, 28 Jul 2016 16:48:43 +0200

Dear amber users,

I am running a QM/MM molecular dynamics simulation and I get the following error message:

 SANDER BOMB in subroutine QM_CHECK_PERIODIC<qm_mm.f>
 QM region + cutoff larger than box
 cannot continue, need larger box.

I understand why this is happening and to solve this behaviour I wish to create a larger water box around my protein rather than decrease the value of the cutoff.

I was thinking to strip all the water molecules and then create a new box and new parameters with tleap but then, if I understand correct, I would have to start all over (starting from 0 ps). So, is there any way such that, I would be able to have a bigger water box and use the restart file from the previous run in order to continue my simulation from where it has been stopped?

Thank you for any help,

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Received on Thu Jul 28 2016 - 08:00:03 PDT
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