On 10/9/16 8:26 PM, Thejus Kartha wrote:
I'm sorry Dr. Lemkul. I thought I put the links for the images I uploaded on Google Drive. Let me try it again. The single molecule: https://drive.google.com/open?id=0B3dugKVFN2ajTmZMYVdOX0NfbGM The system that was generated by genconf:https://drive.google.com/open?id=0B3dugKVFN2ajSDdiampwREVoeUU
Don't use -shuf. You're scrambling your molecules.
Regarding the charges in the topology, I produced them myself using a minimization in Avogadro. I was guessing that was sufficient. It also made sense to me, since dioxane is a polar molecule with non-zero dipole moment. There is no necessity that the system I deal with must have zero charge, is there?
This is wrong. It is a symmetrical molecule and in the absence of an external electric field, will in fact have a zero net dipole moment. It may have non-zero components of the dipole vector, but the total net dipole is zero.
The fractional charges absolutely must sum to zero in this molecule. Ionized molecules can have *integral* charges (-1, +1, etc) but no molecule can have a fractional charge. You can't acquire 46.6% of an electron, can you? That's what your topology is doing.
You should be building this topology based on any available linear or cyclic ether parameters available in GROMOS, or use a force field that you can parametrize more easily.
-Justin
Thank you. Thejus Kartha On Monday, 10 October 2016 5:47 AM, Justin Lemkul <jalem...@vt.edu> wrote: None of your screenshots work; most users receive mail in plain text. If you want to share files or images, upload them somewhere and provide a link. <snip>[ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 903 DOX rtp DOX q -0.5 1 CH2 903 DOX CA 1 0.071 14.027 ; qtot 0.071 2 CH2 903 DOX CB 1 0.071 14.027 ; qtot 0.142 3 CH2 903 DOX CD 1 0.071 14.027 ; qtot 0.213 4 CH2 903 DOX CE 1 0.071 14.027 ; qtot 0.284 5 OA 903 DOX OF 1 -0.375 15.9994 ; qtot -0.091 6 OA 903 DOX OG 1 -0.375 15.9994 ; qtot -0.466This topology is complete nonsense. You have a net charge of -0.466. I don't know where you got those charges, but they make no sense whatsoever. -Justin[ bonds ] ; ai aj funct c0 c1 c2 c3 1 2 2 gb_14 1 6 2 gb_12 2 5 2 gb_12 3 4 2 gb_14 3 5 2 gb_12 4 6 2 gb_12 [ pairs ] ; ai aj funct c0 c1 c2 c3 1 3 1 2 4 1 5 6 1 [ angles ] ; ai aj ak funct c0 c1 c2 c3 2 1 6 2 ga_14 1 2 5 2 ga_14 4 3 5 2 ga_14 3 4 6 2 ga_14 2 5 3 2 ga_9 1 6 4 2 ga_9 [ dihedrals ] ; ai aj ak al funct c0 c1 c2 c3 c4 c5 6 1 2 5 1 gd_1 2 1 6 4 1 gd_2 1 2 5 3 1 gd_2 5 3 4 6 1 gd_1 4 3 5 2 1 gd_2 3 4 6 1 1 gd_2 ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif ; Include water topology #include "gromos43a1.ff/spce.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include "gromos43a1.ff/ions.itp" [ system ] ; Name DIOXANE [ molecules ] ; Compound #mols DOX 1-------------------------------------------------------------------------------------------------------- But, when I use the gmx genconf command to expand it into a collection of molecules (8 x 8 x 8 box), the result contains disordered molecules as seen in my VMD window. However, the .gro file produced after the genconf seems to be looking fine though. The genconf generated system looks like this: Screenshot from 2016-10-10 05-12-09.png As you can see, the molecules are not seen correctly, that is, there are many places where I have an oxygen in the place of carbon, vice-versa, only carbon containing rings, so on and so forth. Can you please let me know what's going on? I mean, there's no reason why gmx genconf shouldn't be just duplicating the molecule I give it. The command I used: gmx genconf -f dioxane.gro -o diox.gro -nbox 8 8 8 -dist 0.3 -shuffle -rot | | | | | | | | | | | Screenshot from 2016-10-10 05-12-09.png | | | | Thanks & regards,Thejus Kartha
-- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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.
