[gmx-users] regarding box volume

2015-08-29 Thread soumadwip ghosh
Ignore the previous mail. Hi, please excuse me if my question appears very silly to you. I have a hybrid of a Carbon nanotube and a polymer and I want to study the unwrapping dynamics of the polymer in presence of a polymer binding agent. I kept the hybrid inside a triclinic box and am doing

Re: [gmx-users] regarding box volume

2015-08-29 Thread Johnny Lu
I am new to simulation and haven't done any simulation for finding free energy. The following is my guess. How big are the molecules? If the box size is small then the concentration of the molecules is higher. May be the dissociation part is fine if: the hybrid can't see its mirror image (the

Re: [gmx-users] regarding box volume

2015-08-29 Thread Justin Lemkul
On 8/29/15 9:37 AM, Johnny Lu wrote: I am new to simulation and haven't done any simulation for finding free energy. The following is my guess. How big are the molecules? If the box size is small then the concentration of the molecules is higher. May be the dissociation part is fine if: the