[gmx-users] molecule breakage during minimization

[Dallas Warren]

The molecules will not be broken, it is a visualisation artifact.

http://manual.gromacs.org/documentation/2018.5/user-guide/terminology.html#periodic-boundary-conditions

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Fri, 3 Jan 2020 at 07:58, Yogesh Sharma <yogesh.rma13 at gmail.com> wrote:

> Hello everyone,
> Before equillibriation I was trying to minimize my protein membrane system.
> energyminimized.gro file  when vizualized in vmd showed few lipid molecules
> broken. Is it safe to use trjconv to make whole molecule after em or i can
> proceed with breakage? This is the minimization.mdp file I am using
> define                  = -DREST_ON -DSTEP6_0
> integrator              = steep
> emtol                   = 1000.0
> nsteps                  = 5000
> nstlist                 = 10
> cutoff-scheme           = Verlet
> rlist                   = 1.2
> vdwtype                 = Cut-off
> vdw-modifier            = Force-switch
> rvdw_switch             = 1.0
> rvdw                    = 1.2
> coulombtype             = pme
> rcoulomb                = 1.2
> ;
> constraints             = h-bonds
> constraint_algorithm    = LINCS
> --
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