Hi, I would like to post a question about simulating with "Walls" in gromacs. The question is very simple. I am trying to simulate a simple box of water molecules with pbc=xy and walls at z=0 and z=z_box. I use Berendsen T-coupling and no pressure bath. I am trying:
pbc=xy nwall =2 wall_atomtype = C1 C1 (C1 are the alkane carbons defined in the martini force field file) wall_type = 9-3 wall_density = 110 110 wall_r_linpot = 1 and all what I have is that the initial box of water molecules breaks in two pieces that separate each other in the z-direction. The same result (or a segmentation fault) is obtained by using 10-4 o 12-6 LJ potentials, large wall_r_linpot values, other values of wall_densities, so I think that the problem is with the wall_atomtype. I tried the water bead (W) instead, and segmentation fault is obtained. thank you very much in advance, Ramon Aquest correu electrònic i els annexos poden contenir informació confidencial o protegida legalment i està adreçat exclusivament a la persona o entitat destinatària. Si no sou el destinatari final o la persona encarregada de rebre’l, no esteu autoritzat a llegir-lo, retenir-lo, modificar-lo, distribuir-lo, copiar-lo ni a revelar-ne el contingut. Si heu rebut aquest correu electrònic per error, us preguem que n’informeu al remitent i que elimineu del sistema el missatge i el material annex que pugui contenir. Gràcies per la vostra col·laboració. Este correo electrónico y sus anexos pueden contener información confidencial o legalmente protegida y está exclusivamente dirigido a la persona o entidad destinataria. Si usted no es el destinatario final o la persona encargada de recibirlo, no está autorizado a leerlo, retenerlo, modificarlo, distribuirlo, copiarlo ni a revelar su contenido. Si ha recibido este mensaje electrónico por error, le rogamos que informe al remitente y elimine del sistema el mensaje y el material anexo que pueda contener. Gracias por su colaboración. This email message and any documents attached to it may contain confidential or legally protected material and are intended solely for the use of the individual or organization to whom they are addressed. We remind you that if you are not the intended recipient of this email message or the person responsible for processing it, then you are not authorized to read, save, modify, send, copy or disclose any of its contents. If you have received this email message by mistake, we kindly ask you to inform the sender of this and to eliminate both the message and any attachments it carries from your account. Thank you for your collaboration. -- 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.
