[gmx-users] NPT Equilbration fails

Mark Abraham mark.j.abraham at gmail.com
Tue Aug 23 18:40:02 CEST 2016


What box dimensions should be appropriate for the density of such a mixture?


On Mon, Aug 22, 2016 at 4:54 PM Apramita Chand <apramita.chand at gmail.com>

> Dear All,
> I'm trying to create a pre-equilbrated urea-water box to solvate my peptide
> with, using GROMOS53a6 parameters.  I have 10 urea molecules and I want the
> number of solvent molecules to be 489 in this box ( I use maxsol for this
> purpose) . I'm putting the box sizes in the range 2.5-3.0 repeatedly and
> carrying out minimization and NVT equilbration without any problem.
> But the NPT Equilbration crashes with the error:
> *One of the box vectors has become shorter than twice the cut-off length or
> box_yy-|box_zy| or box_zz has become smaller than the cut-off.*
> I can't tamper with the specified cutoffs like rvdW=1.4. So I have tried
> several box sizes and all of them have this problem . I tried changing box
> type from cubic to dodecahedron but to no avail.
> What should I do to overcome this problem?
> yours sincerely
> Apramita Chand
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