[gmx-users] Re: water dimer is gas phase

[Vitaly Chaban]

>
> For vacuum systems, "pbc = no" in conjunction with zero cutoffs is correct
> to obtain a gas-phase system.


For reasonably large box, this is the same heck.

Nilesh: visualize your system, using VMD or ngmx. The behavior of your
molecular cluster during the first ps will provide an answer. Are you
sure that your topology is healthy?



-- 
Dr. Vitaly V. Chaban, Department of Chemistry
University of Rochester, Rochester, New York 14627-0216


>The system has clearly exploded.  To
> diagnose, I would suggest:
>
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>