[gmx-users] angle_restraints_z and -ddcheck

I have determined that the proper solution here is to use particle decomposition. -noddcheck simply delays the inevetable fatal LINCS error. Nevertheless, mdrun -pd requires that one maintains whole molecules in the starting conformation: http://lists.gromacs.org/pipermail/gmx-users/2010-Ja

[gmx-users] angle_restraints_z and -ddcheck

Hello, I have just started working with the [ angle_restraints_z ] portion of the code. My initial tests indicate that it works in my system. However, in some cases I am getting a fatal error that a pair interaction is too far apart to be calculated within domain decomposition. Although t

RE: [gmx-users] [ angle_restraints_z ]

er of magnitude. Berk Date: Tue, 20 May 2008 16:39:22 +0430 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: Re: [gmx-users] [ angle_restraints_z ] Dear Berk, Thanks for the reply. Yes. In fact I made the choice of multiplicity=1 based on the explanation in eq. 4.68: "A multiplic

Re: [gmx-users] [ angle_restraints_z ]

ECTED]> wrote: > > > > > -- > Date: Sat, 17 May 2008 08:48:28 +0330 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: [gmx-users] [ angle_restraints_z ] > > > Hi all, > > There are atoms (a1 and a2) in my small molecu

RE: [gmx-users] [ angle_restraints_z ]

Date: Sat, 17 May 2008 08:48:28 +0330 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: [gmx-users] [ angle_restraints_z ] Hi all, There are atoms (a1 and a2) in my small molecule coordinate file that have the same z component: a1: atom#22 (x1,y1,60.231) a2: atom#45 (x2

[gmx-users] [ angle_restraints_z ]

Hi all, There are atoms (a1 and a2) in my small molecule coordinate file that have the same z component: a1: atom#22 (x1,y1,60.231) a2: atom#45 (x2,y2,60.231)If I use these lines only Therefore the vector a1-a2 makes theta=90o with the z-axis. in my previous MD runs the a1-a2 were flexible (the