[gmx-users] Orthorhombic structure and Lincs warnings

Alex 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
rectangular box?
2. Why are you using LINCS with graphene, which should _not_ be simulated
with constraints?
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
> parallelogram.
> 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
> everytime.
> 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.
> Regards
> Sagar
> --
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list