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