Re: Solvent Box

From: Vibhor Agrawal (
Date: Wed Jun 26 2013 - 12:19:54 CDT

run your simulation little more longer


On Wed, Jun 26, 2013 at 1:18 PM, Ivana <> wrote:

> Try to minimize more.
> On 26 June 2013 14:15, Jon Kusner <> wrote:
>> Hello,
>> We have been trying to create an acetonitrile solvent box. We have been
>> following the instructions of other troubleshooters and looking on other
>> forums for guidance but have still not been successful. Currently we have a
>> psf of our final solvent box, a 12x12x12 array of acetonitrile molecules,
>> that we are trying to equilibrate. Whenever we try to run
>> an equilibration we get through 3000 step of minimization but as soon as
>> the program begins molecular dynamics we receive the error:
>> Fatal error on PE 2> Fatal Error: Periodic cell has become too small for
>> original patch grid!
>> Possible solutions are to restart from a recent checkpoint, increase
>> margin, or disable useflexiblecell for liquid simulation.
>> We have tried each of these possible solutions and received the same
>> result. If there is any guidance we could receive it would be much
>> appreciated. Thank you for all of your help.
>> Best,
>> Jon

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