I created a rectangular ensemble consist of crystalline erythritol molecules. I want to create a liquid-solid interface through annealing, making half of the ensemble amorphous and keep the other half crystalline.
This is how I did it：create a eryt.itp with [ moleculetype ] eryt, that is identical to my original erythritol.itp ([ moleculetype ] erythritol) constructed by msi2g96, then change the name of the molecules which I want to fix from erythritol to eryt in in.g96. My topology file is as below,
#include "oplsaaff.itp"
#include "eryt.itp"
#ifdef POSRES
#include "posre.itp"
#endif
#include "erythritol.itp"
[system]
crystal
[molecules]
eryt 432
erythritol 432
However, all the erythritol molecules became constrained. Can anyone tell me what I did wrong, and how to fix it?
Dear Hsin-Ru
please see this tutorial about two-phase simulation:
http://www.mdtutorials.com/gmx/biphasic/index.html
you could insert "eryt" molecules which are fixed in half of box with "gmx insert molecules" and then 432 erythritol in another half of simulation box.
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