[gmx-users] using enegygrps

[kordzadeh at aut.ac.ir]

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?

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 .

Thank you very much for your time and your answer

Regards

Azadeh

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