Hi gromacs users, I was able to simulate graphene sheet in water. Now I want to simulate functionalised graphene sheet with -OH groups attached randomly to graphene sheet. I modified atomname2type.n2t file by adding oxygen and hydrogen groups to it. Following is my .n2t file:
C opls_995 0 12.011 2 C 0.142 C 0.142 C opls_996 0 12.011 3 C 0.142 C 0.142 C 0.142 C opls_997 0 12.011 1 C 0.142 C opls_998 0 12.011 4 C 0.142 C 0.142 C 0.142 O 0.143 OH opls_154 -0.7 15.9994 2 C 0.143 HO 0.96 HO opls_155 0.435 1.008 1 OH 0.96 But when I give following x2top command, I get error message : g_x2top -f grap1.pdb -o graphene.top -name GRA -nexcl 3 -pbc Error: Fatal error: Could only find a forcefield type for 256 out of 456 atoms Can anyone please let me know what can be creating the problem? Thanks and Regards Sukriti Gupta Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798 Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web:erian.ntu.edu.sg ________________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin Lemkul <jalem...@vt.edu> Sent: Thursday, July 17, 2014 7:50 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Graphene topology file On 7/17/14, 7:16 AM, #SUKRITI GUPTA# wrote: > Hi gromacs users, > > I read that for slab geometries where you need pbc in xy, you can use pbc=xyz > and have a slab of vacuum > in between the periodic images in z and use ewald3dc (Yeh and Berkowitz > method). So I changed my mdp file extended my box in z direction( with no > solvent molecules) and did the energy minimization and npt again. In em, the > box looks fine but with npt again I get same output i.e. water molecules fly > away and box size in z direction increases drastically, through the vacuum > layer is still maintained. Then I changed my pressure coupling to Parinello- > Rahman instead of Berendsen. This time npt runs some steps and gives an error > message: > > Fatal error: > One of the box vectors has become shorter than twice the cut-off length or > box_yy-|box_zy| or box_zz has become smaller than the cut-off. > > Can anyone please let me know how can I solve this problem. If we have a > layer of vacuum, wont the box size reduce in npt and cause this error? Should > I skip npt and directly do nvt? > If you need to maintain a vacuum layer, your box needs to be incompressible along that direction, i.e. use semiisotropic coupling and set compressibility = 0 in the .mdp file for the z-direction. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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. -- 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.
