Re: [gmx-users] about the bond connection between different groups

Dear Yang, It appears that you will either need to either A) create a new index file using the make_ndx utility, or B) modify your existing index file. If you haven't done this procedure before, the first option may be the easiest. A good description of make_ndx is contained in the manual as

[gmx-users] Ewald summation: n=0

= no pbc = xyz coulombtype = Ewald ;fourierspacing = 0 ewald_rtol = 1e-5 fourier_nx= 0 fourier_ny= 0 fourier_nz= 0 pcoupl = no Thank you, Steve Fiedler

[gmx-users] Segmentation fault in g_traj with -mol opion

with this problem would be appreciated. Thank you, Steve Fiedler conf.gro Helium 2 1HEL He1 1.000 1.000 1.000 2HEL He2 2.000 2.000 2.000 5.0 5.0 5.0 grompp.mdp --

Re: [gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance

oblem. I am quite appreciative of the attention that this issue has received. If there is continued interest, and a willingness for an engineer to receive the topology file in a less public forum than bugzilla, I believe we could proceed with the debugging process. Thank you, Steve Fiedler

Re: [gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance

relatively unchanged upon "recentering", however it is still susceptible to the problem that is the subject of this discussion. If I can reproduce this phenomenon with a publicly available topology file, I can provide the necessary input files for inspection. Thank you again, Steve

Re: [gmx-users] Segmentation fault preprocessing with pull_geometry = cylinder

ompp output appears to have advanced by one > line (output below), however the process still terminates with a > segmentation fault. Additional suggestions or ideas for diagnostics > would be appreciated. > > Thank you, > > Steve Fiedler > > Bottom 3 lines of grompp output: &

Re: [gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance

ystem constructed with a single dummy particle permeant. I appreciate the help of Berk, and Chris' detailed suggestions with this interesting problem. Sincerely, Steve Fiedler Berk Hess wrote: Hi, I just found out that I introduced a bug in 4.0.3, which could cause the pull code t

Re: [gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance

ved outside the box in the x-y plane. The coordinate, topology, and run control parameter file are given below. If there are additional suggestions, I would be greatly appreciative. Thank you, Steve Fiedler - conf.gro Three atoms 3 1AAA A1 1.500 1.500

[gmx-users] Segmentation fault preprocessing with pull_geometry = cylinder

appreciated. Thank you, Steve Fiedler Bottom 3 lines of grompp output: Using a fourier grid of 27x36x63, spacing 0.119 0.117 0.120 Pull group natoms pbc atom distance at start reference at t=0 Segmentation fault *Berk Hess* gmx3 at hotmail.com <mailto:gmx-users%40gromacs.org?Subj

[gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance

he mdp file are listed below, as well as the contents of the ppa file which has worked previously. Suggestions would be appreciated, Thank you, Steve Fiedler Gromacs 4.0.0 mdp pull options pull = constraint pull_geometry = distance pull_dim = N N Y pull_start = no pull_init1 = .4 pu

[gmx-users] Segmentation fault preprocessing with pull_geometry = cylinder

sion 3.3.3 with the below ppa file options. Suggestions would be appreciated. Thank you, Steve Fiedler Gromacs 4.0.3 mdp pull options: pull = constraint pull_geometry = cylinder pull_r1 = 1 pull_r0 = 1.5 pull_dim = N N Y pull_vec1 = 0 0 1 pull_group1 = Buk pull_group0 = Ref pull_init1 = .

Re: [gmx-users] Pull code with shuffle/sort options

Thank you Chris for providing recognition of this issue. -Steve Chris Neale wrote: I have encountered noticeable differences while using the pull code with the -shuffle -sort options in parallel, as opposed to running in serial or in parallel without the options. Using -shuffle -sort, the dy

[gmx-users] Pull code with shuffle/sort options

= 0 0 0.0 and the programs are invoked with: grompp_d -sort -shuffle -np 4 mpirun -np 4 mdrun_d -v -pi pull.ppa -pn index.ndx Regards, Steve Fiedler ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Ple

Re: [gmx-users] Missing LJ interaction

David van der Spoel wrote: Steve Fiedler wrote: Thank you for looking over the input and for suggestions Mark. Unfortunately, a comparison of the topologies with diff revealed no inconsistencies. GROMACS can correctly recognize the presence of the significant repulsion (e+10) between atoms

Re: [gmx-users] Missing LJ interaction

tes were taken from a calculation of membrane system just before a crash, I believe it is this lack of intermolecular nonbonding repulsion responsible for allowing atoms 1 and 5 to get this close in the first place. Again, any insights are most welcome. Steve Mark Abraham wrote: Steve Fied

[gmx-users] Missing LJ interaction

Dear all, I have encountered an unexpected behavior in which nonbonding values for close intermolecular pairs do not appear to be always present. I have reduced this problem to the configurational energy of two triatomic isomers. The LJ values correctly rise ten orders of magnitude upon del