[gmx-users] NPT Equilbration fails

Apramita Chand apramita.chand at gmail.com
Mon Aug 22 16:54:17 CEST 2016

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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