Re: [gmx-users] Debugging 'inconsistent shifts'

On 1/14/15 4:44 PM, Kalev Takkis wrote: Hi, list! GROMACS complains about inconsistent shifts and suggests me to check my topology. I have so done, but the problem is not immediately obvious. How can I make it tell me exactly which atoms/bonds it finds faulty? What were you doing when the

[gmx-users] Re PME question in GMX4.6.5

Mark, Thanks for your reply! I actually found this disscussion about PME, which might be from you? https://groups.google.com/forum/#!topic/archive-gmx-users/VmK7H5vF9cY you were saying:The total energy for that interaction is distributed over the Coul-SR and *Coul. recip terms (which is how PME

[gmx-users] Debugging 'inconsistent shifts'

Hi, list! GROMACS complains about inconsistent shifts and suggests me to check my topology. I have so done, but the problem is not immediately obvious. How can I make it tell me exactly which atoms/bonds it finds faulty? All the best, Kalev Takkis Institute of Chemistry Faculty of Science and

[gmx-users] results produced by auto-tuning of Coulomb cut-off/grid for PME can not be reproduced by manually setting the Coulomb cut-off and grid spacing

Dear GMX developers, I've encounter a problem in GROMACS concerning the auto-tuning feature of PME that bugged me for months. As stated in the title, the auto-tuning feature of mdrun changed my coulomb cutoff from 1.4 nm to ~3.3 nm (stated in md.log) when I set -npme to be 28 (128 total CPU

Re: [gmx-users] analysing charmm trajectories

Dear Justin, I removed the cmap tems form the .top file as you suggested and the problem is now solved. Thanks a lot for your precious help. Chiara 2015-01-14 0:42 GMT+01:00 Justin Lemkul jalem...@vt.edu: On 1/13/15 8:18 AM, Chiara Parravicini wrote: Dear all, I'd like to use the

[gmx-users] Distance restraint file error

Please help me out I have got some error while analyzing my molecular dynamics output for violations from NMR data. I have used g_disre option but I get this as ann error pop up *Program g_disre_d, VERSION 4.6Source code file: /data/software/gromacs-4.6/src/tools/gmx_disre.c, line:

Re: [gmx-users] trjconv mismatch

Hi Jennifer, You can extract the first frame using the same logic and save it as PDB/GRO. Then you can use that structure as reference for the second pass. However, in this case it seems more logical to just write out a PDB trajectory directly and use 'cat' to combine them in a single file. Hope

[gmx-users] trjconv mismatch

Dear All, I have got this error while running trjconv from .xtc to .pdb file. The System includes 8 Protein (4622 Atoms each, x8 = 36976 Atoms). 135978 is the total number of Atoms in the System. The index.ndx was created from md.gro file, and I Chose #1 for Protein. I don't know where is the

Re: [gmx-users] trjconv mismatch

On Wed, Jan 14, 2015 at 9:00 AM, Jennifer Vo quyvio...@gmail.com wrote: Dear All, I have got this error while running trjconv from .xtc to .pdb file. The System includes 8 Protein (4622 Atoms each, x8 = 36976 Atoms). 135978 is the total number of Atoms in the System. The index.ndx was created

Re: [gmx-users] Using -all flag in g_angle command

gmx angle -h suggests -ov -all generates multiple graphs, only the first of which is the average. What's in the rest of your output file? Mark On Wed, Jan 14, 2015 at 7:21 AM, GAYATHRI S gayathr...@iitb.ac.in wrote: Hello everyone, I simulated an NADH molecule. I want to check how each of

Re: [gmx-users] Gromacs precision and the precision of values set in the mdp file

On Wed, Jan 14, 2015 at 12:39 AM, Eric Smoll ericsm...@gmail.com wrote: Hello Gromacs users, What is the precision limit for values entered in an mdp file for a single precision gromacs simulation? For mixed precision probably float. Does this increase when using gromacs is compiled in

Re: [gmx-users] trjconv mismatch

Dear Mark, Many thanks for your reply. My command was: trjconv_mpi -f md-*.trr -n index.ndx -timestep 100 -o md-*-timestep100.xtc for every trr file, then concatenate by using trjcat_mpi -f md-*-timestep100.xtc -n index.ndx -o md-timestep100.xtc For index.ndx: make_ndx_mpi -f md.gro -o

Re: [gmx-users] Error message in GROMACS

On 2015-01-14 10:22, Deep Bhattacharya wrote: Respected Sir, I have read up a lot on GROMACS webpages and the problems answered by you are extremely helpful. I have been facing this problem in computing violations of distance restraints and I get this error message , I will be extremely glad

[gmx-users] [MGMS-DS]: Molecular Modelling Workshop March 9-11, 2015 in Erlangen, Germany

Dear list subscribers, I am very happy to announce that also this year, the traditional Molecular Modelling Workshop in Erlangen takes place on March, Monday 9th to Wednesday 11th, 2015. Starting on Monday after lunch should allow to avoid travelling on weekend keeping the expenses

[gmx-users] Cluster studies of ions

Dear gromacs users, I am trying to study the cluster formation behavior of oppositely charged ions in water. While analyzing the box, it appears that cations and anions forms chains in the solution like C+A-C+A- I want to quantify the amount of this chain formation, like whether its dimer

[gmx-users] g_rotacf lag time

Dear list, is there a way to define the lag time for the auto correlation function in g_rotacf? Thank you very much, Max -- 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