[gmx-users] Orthorhombic structure and Lincs warnings
nedomacho at gmail.com
Wed Sep 5 21:45:49 CEST 2018
It's not the first time you're posting this message and there's a reason
noone is replying.
1. What are the inter-axis angles of that orthorhombic box? Why not a
2. Why are you using LINCS with graphene, which should _not_ be simulated
3. Why are you restraining your system on top of everything else?
4. Did you verify that your graphene model (without constraints or
restraints) was stable prior to adding water?
On Wed, Sep 5, 2018 at 1:35 PM sagar bathla <sagarbathla4 at gmail.com> wrote:
> 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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