[gmx-users] Orthorhombic structure and Lincs warnings

sagar bathla sagarbathla4 at gmail.com
Wed Sep 5 21:35:17 CEST 2018

Dear all,

Can simulation for orthorhombic structure be done in gromacs?
Actually I am working with 2-D graphene sheets which are like a

In my system, there is a graphene sheet (restrained)and water.
After the energy minimization, energy is coming positive (order of 10^8)
On Visualization in vmd, the structure appears to be rectangle and there
comes a warning with it

152 inconsistant shifts etc.

When I am trying to equillibrate the system then so many lines warnings
appears of rotation of bonds more than 90 degrees and simulation crashes

Is there any problem with structure or y else?
Earlier also I posted this but issue hasn't resolved yet.

Please help me to find this problem.


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