[gmx-users] Expansion system after NVT Equilibrium in Gromacs

Justin Lemkul jalemkul at vt.edu
Tue Nov 13 00:59:14 CET 2018

On 11/11/18 12:16 PM, yasminesophi at students.itb.ac.id wrote:
> i'm currently running a simulation protein in water using gromacs with force field gromos96 54a7. the protein structure that i used is from modeller. there is no problem untill the minimization step but the system is expanding after NVT equilibration. and when i try to do NPT equilibration after that, the system is shrinking [the box volume is smaller than before]
> i'm using the parameter from gromacs tutorial "lysozyme in water" with hbonds constraints for NVT equilibration and the temperature is 298 K. please help me to solve this problem

Don't use input files from my tutorial if you're using GROMOS. The 
nonbonded settings and required constraints are different, as hopefully 
I make very clear...

In any case, if you're running NPT, naturally the system will expand and 
contract. There's no reason that it won't, as that is precisely what a 
barostat does. If your system is changing, that just means your initial 
conditions are not compatible with the specified NPT ensemble and the 
properties of the system have to adjust.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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