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

Justin A. Lemkul jalemkul at vt.edu
Thu May 19 22:42:13 CEST 2011

Vitaly Chaban wrote:
>> 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.

Setting a box size and using "pbc = xyz" precludes the use of infinite cutoffs, 
which should be the most rigorously correct way to treat this type of system. 
With PBC, there are long-range effects that should be avoided.

> 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?

I agree with this.  The system should be going absolutely haywire :)



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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