Re: [gmx-users] MD workstation for Gromacs

Thank you Szilárd, So I would be really thankful if you could tell me which configuration is the best: 2x GTX 980 2x GTX 780 Ti 2x GTX Titan Black Sincerely, Sent with MailTrack On Mon, Oct

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 wrote: > Dear Gromacs Users > > I would like to analyze frame number 150 to 160 out of 1000 frames. I have > been tr

[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 sear

[gmx-users] Integrity of .trr file + center coordinates

Hello Gromacs users, Beyond gmxcheck, how can I evaluate the integrity of a .trr file? I have a .trr file that I am having difficulty postprocessing. I would like to fix the cog/com in the center of the simulation box. trjconv -center is not working. Is there some alternative? Best, Eric -- Gro

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.) But

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 wo

Re: [gmx-users] Time averaged ramachandran plot

On 10/26/14 5:14 PM, Sanku M wrote: 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

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] Umbrella Sampling tutorial by Dr. Justin Lemkul

On 10/26/14 4:32 PM, Agnivo Gosai wrote: 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 c

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 parallelise

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 trajco

Re: [gmx-users] how to make statistics?

Hi, What does gmx hbond -h suggest to you? Mark On Oct 26, 2014 5:16 PM, "Albert" wrote: > 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 ma

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" wrote: > Hello Gromacs users, > > I have a trajectory file script18_o.trr that I am trying to proc

[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 to

[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] 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] 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 quic

[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 bef

[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] 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 http://www.gromacs.org/Support/Ma

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 i

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 th

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 wrote: > > > On 10/24/1

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 wrote: > Hi, > > I have a system consists of a box of water and a monolayer of polymer in > t