On 2/15/18 4:17 AM, kordza...@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 -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
