Re: [gmx-users] Simulating Multiple Solute Particles

Hi - genbox must work. You add the first molecule, then the second molecule and so on. So, I suggest to run genbox for a few times and have enough empty space available in the box. Otherwise, there is a wonderful tool called PACKMOL. The acid molecule looks pretty sexy. I guess it will not be

Re: [gmx-users] Cannot combine residue position based cog selection with index output for g_select

Hi, I'm not the expert here, but I think that gmx select -selrpos has options that you should be able to use here. See gmx help selections positions Mark On Fri, Oct 24, 2014 at 10:43 PM, Huang Dongxu fred...@gmail.com wrote: Hi, I have a system consists of a box of water and a monolayer of

Re: [gmx-users] error in the middle of running mdrun_mpi

Thanks Justin. I have increased the cutoff, and yeah thats work. There were no error message anymore. The first 6 nanoseconds, i felt the simulation run slower. Felt so curious that simulation run very fast the rest of time. On Fri, Oct 24, 2014 at 7:37 PM, Justin Lemkul jalem...@vt.edu wrote:

Re: [gmx-users] error in the middle of running mdrun_mpi

On 10/26/14 9:17 AM, Nizar Masbukhin wrote: Thanks Justin. I have increased the cutoff, and yeah thats work. There were no error message anymore. The first 6 nanoseconds, i felt the simulation run slower. Felt so curious that simulation run very fast the rest of time. Longer cutoffs mean

Re: [gmx-users] error in the middle of running mdrun_mpi

regarding gaining speed in implicit solvent simulation, i have tried to parallelize using -ntmpi flag. However gromacs doesn't allow as i use group cutoff-scheme. Any recommendation how to parallelise implicit solvent simulation? I do need parallelise my simulation. I have found the same question

[gmx-users] histo-clust.xvg from g_clustsize

Does anyone happen to remember what the frequencies in histo-clust.xvg from g_clustsize mean? Are they directly comparable between different systems? Dr. Vitaly V. Chaban Виталий Витальевич ЧАБАН -- Gromacs Users mailing list * Please search the archive at

[gmx-users] g_distMat: A tool to calculate average min-distance matrix on multiple CPU cores

Dear GROMACS Users, I have wrote a small tool g_distMat (https://github.com/rjdkmr/g_distMat). It is almost similar to the g_mdmat. Features: Average minimum-distance matrix (residue-wise) between two index groups Related Standard deviation and variance matrix Fraction of Contacts(map) over

[gmx-users] how to make statistics?

Hello: I am going to make statistics for how much percentage H-bond formed for residue A and B. I am just wondering how can we to do this? thank you very much. Albert -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

[gmx-users] trjconv gets stuck on frame

Hello Gromacs users, I have a trajectory file script18_o.trr that I am trying to process. Using gmxcheck, this file appears to be complete. When I execute the command below trjconv -f ../script18/script18_o.trr -s ../script17/script17_o.tpr -o tmp1.trr -pbc whole EOF 0 EOF the code moves

[gmx-users] Selecting box dimension and COM position - Pull Code

Dear Users I have gone through the tutorial on umbrella sampling by Dr. Lemkul and am using the methodology described therein for running my own simulations. It is explained that :- GROMACS calculates distances while simultaneously taking periodicity into account. This, if you have a 10-nm box,

[gmx-users] Umbrella Sampling tutorial by Dr. Justin Lemkul

Dear Users I am following the Umbrella Sampling tutorial by Dr. Lemkul and would like to have one of my doubts addressed :- After using pdb2gmx on the supplied pdb file , a topology file is obtained specifying the topology files for different protein chains in .itp format.. Inside the .itp files

[gmx-users] Time averaged ramachandran plot

Hi  I plan to plot the ramachandran plot of all the dihedral angles each of which is averaged over time-frames of trajectories. But, I find g_rama or g_chi gives the time profile of ramachandran plot. But, if I want to plot the time-averaged Phi.Psi angles of all residues, is there any method

Re: [gmx-users] trjconv gets stuck on frame

Hi, The output does drop in frequency at some point, so that might be all you are seeing. Experiment with -b and values around the putative problem area. Mark On Oct 26, 2014 6:59 PM, Eric Smoll ericsm...@gmail.com wrote: Hello Gromacs users, I have a trajectory file script18_o.trr that I am

Re: [gmx-users] trjconv gets stuck on frame

Hi Mark, Thank you for responding so rapidly. I should note that identical processing (I use a script) on the trajectories produced by slightly different chemical systems had no problem and trajconv produced a complete processed trajectory. However, when processing the problematic few with

Re: [gmx-users] error in the middle of running mdrun_mpi

On 10/26/14 9:55 AM, Nizar Masbukhin wrote: regarding gaining speed in implicit solvent simulation, i have tried to parallelize using -ntmpi flag. However gromacs doesn't allow as i use group cutoff-scheme. Any recommendation how to parallelise implicit solvent simulation? I do need

Re: [gmx-users] Selecting box dimension and COM position - Pull Code

On 10/26/14 3:43 PM, Agnivo Gosai wrote: Dear Users I have gone through the tutorial on umbrella sampling by Dr. Lemkul and am using the methodology described therein for running my own simulations. It is explained that :- GROMACS calculates distances while simultaneously taking periodicity

Re: [gmx-users] Simulating Multiple Solute Particles

Thanks for your help. And actually my version of gromacs does not have genbox anymore. (http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0 at the bottom: GENBOX - This tool has been split to gmx solvate and gmx insert-molecules.) But it's no big deal, insert-molecules seemed to

Re: [gmx-users] Simulating Multiple Solute Particles

On 10/26/14 10:49 PM, Nathan K Houtz wrote: Thanks for your help. And actually my version of gromacs does not have genbox anymore. (http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0 at the bottom: GENBOX - This tool has been split to gmx solvate and gmx insert-molecules.)

[gmx-users] How to save trajectories of our interest into vmd

Dear Gromacs Users I would like to analyze frame number 150 to 160 out of 1000 frames. I have been trying to load frames of my interest into vmd. But I was not able to do it. Please tell me how to use it. Thanks in advance Surya Graduate student India -- Gromacs Users mailing list * Please

Re: [gmx-users] How to save trajectories of our interest into vmd

Dear Suryanarayana, Try this, I hope it will help g_rmsf -f file.trr -s file.tpr -res -b 150 -e 160 -ox Required_frame.pdb On Mon, Oct 27, 2014 at 10:55 AM, Seera Suryanarayana paluso...@gmail.com wrote: Dear Gromacs Users I would like to analyze frame number 150 to 160 out of 1000 frames.