[gmx-users] using enegygrps

Justin Lemkul jalemkul at vt.edu
Thu Feb 15 14:29:56 CET 2018

On 2/15/18 4:17 AM, kordzadeh at aut.ac.ir wrote:
> Hi Dr.Lemkul
> you said, the breaking molecule occured because of period boudary condition, isn't it a problem?
> because before your answer I thought I must select bigger box in order to the breaking won't occur. but now I understand the beaking isn't a problem.
> I have another question, what is difference between LJ-14 and LJ-SR, I think LJ-SR is short range interaction and LJ-14 is long range, am I right?

No. LJ-14 are intramolecular pair interactions (1-4 interactions).

> I have a 128 DPPC, one drug molecule and 19110 water molecule in my box. when I select LJSR-SOL-SOL , then I will get vdw interaction between water molecules,
> but when I  select LJSR:drug-drug, will I  get vdw interaction between atoms of drug? because there is only  one drug molecule in my box .

Yes, if there are interactions that are within the short-range cutoff 
but not included in the 1-4 pair list.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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