On 2/20/18 1:47 PM, Ahmed Mashaly wrote:
Hi About the restrains, I see that it is necessary for NVT and NPT. For the .top and .gro produced by Acpype, https://drive.google.com/open?id=1K5IqAWb1_jXUfUPDjDtkOX2l8GuzbprM I don't have porse.itp nor anything related to restrain in the .top file, only for water #ifdef FLEXIBLE [ bonds ] ; i j funct length force.c. 1 2 1 0.09572 462750.4 0.09572 462750.4 1 3 1 0.09572 462750.4 0.09572 462750.4 So what shall I do in this case? and what is the ideal time for NVT and NPT
Restraints are typically applied to solute heavy atoms to prevent distortion from initial, artificial configurations. It is very rare to need to restrain water, as that defeats the purpose of equilibration, which is primarily to allow the solvent to relax and achieve the desired state.
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