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

Hello everyone, I simulated an NADH molecule. I want to check how each of the dihedral angles changes during the simulation. In other words, I want to plot a graph of individual (not average) dihedral angles versus time. To do so, I created an index file using the following command: $ mk_angndx

Re: [gmx-users] Applying restraints into 'secondary structure' of a Protein

Dear Mark, Thanks for your reply. Does it do that in just-water also? If the structure is not rock-stable in water, then your required minimum amount of sampling goes up immensely, because you will have to sample many such transitions to observe adsorption (when/if it happens). Yes it does. The

Re: [gmx-users] clustering using gromos method

Thanks for the reply Xavier. Cheers, Adriana *** Dra. Adriana D. Garro Química Medicinal Facultad de Química, Bioquímica y Farmacia Universidad Nacional de San Luis IMASL-CONICET San Luis, Argentina Tel..:+54 266 4424689 int

Re: [gmx-users] clustering using gromos method

Yes, should work. Check that the central structures make sense. At some point this option was not giving the correct structure. On Jan 13, 2015, at 1:32 PM, Adriana Garro adrianagarr...@gmail.com wrote: Another question just to be sure that I get what I want. I want the structure with the

Re: [gmx-users] Transition matrix generation

On Jan 13, 2015, at 1:27 AM, pratibha kapoor wrote: Hi, I have done MD simulations on my system and have generated clusters of my interest. Now, I would like to look at the transitions between different clusters and henceforth the most probable pathway. Is there any inbuild software that can do

[gmx-users] Virial Calculation in Gromacs Source Code

Dear All, As part of my work I am looking at making modifications to calculation of the virial in gromacs. I have spent some time making myself a bit familiar with the gromacs source and I've looked at the doxygen generated docs and through the various pages on the developer section of the

Re: [gmx-users] clustering using gromos method

Another question just to be sure that I get what I want. I want the structure with the smallest average distance to the others (The center of a cluster) for each cluster written in the clusters.pdb file (option -cl), but after calculation I get this message in the log file Writing middle

[gmx-users] analysing charmm trajectories

Dear all, I'd like to use the gromacs analysis tool to analyse a simulation performed with charmm. I installed the latest gromacs version (5.0.4), in which both .dcd trajectories and all the files read also by vmd should be readable. After that, the trajectory is correctly processed by gromacs,

[gmx-users] trjconv mismatch in number of atoms

Dear Experts, I am running a trjconv from xtc files to pdb file but have got this error: Fatal error: Index[4622] 135978 is larger than the number of atoms in the trajectory file (36976). There is a mismatch in the contents of your -f, -s and/or -n files. I don't know where the origin of the

[gmx-users] Pressure coupling error

Hi all, I’m receiving this error from grompp: ERROR 1 [file npt.mdp, line 50]: Pressure coupling not enough values (I need 2) I think I’ve inserted in the .mdo the required values: integrator = md tinit= 0 dt = 0.002 nsteps

Re: [gmx-users] Pressure coupling error

You also need to add a second value for compressibility as you have done for tau-p and ref-p. Adam Hardy PhD Student School of Engineering and Physical Sciences Heriot-Watt University Edinburgh EH14 4AS, UK From:

Re: [gmx-users] Virial Calculation in Gromacs Source Code

Hi, No doubt you've seen Appendix B of the manual. (Yes, we need to work more on docs organization.) Relevant data structures and functions mostly include the letters fshift for shift forces. The use of git grep is very much your friend here. Mark On Tue, Jan 13, 2015 at 3:22 PM, Hardy, Adam

Re: [gmx-users] Pressure coupling error

Now it works. Thank you -Original Message- From: Hardy, Adam Sent: Tuesday, January 13, 2015 4:57 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Pressure coupling error You also need to add a second value for compressibility as you have done for tau-p and ref-p. Adam Hardy

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

Hello Gromacs users, What is the precision limit for values entered in an mdp file for a single precision gromacs simulation? Does this increase when using gromacs is compiled in double precision? Best, Eric -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] trjconv mismatch in number of atoms

On 1/13/15 10:15 AM, Jennifer Vo wrote: Dear Experts, I am running a trjconv from xtc files to pdb file but have got this error: Fatal error: Index[4622] 135978 is larger than the number of atoms in the trajectory file (36976). There is a mismatch in the contents of your -f, -s and/or -n

Re: [gmx-users] analysing charmm trajectories

On 1/13/15 8:18 AM, Chiara Parravicini wrote: Dear all, I'd like to use the gromacs analysis tool to analyse a simulation performed with charmm. I installed the latest gromacs version (5.0.4), in which both .dcd trajectories and all the files read also by vmd should be readable. After that,