[gmx-users] g_cluster error

Hello all, I have done two independent GROMACS run for same protein system. I would like to cluster and do further analyses. I used the following commands: 1. g_rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -f2 md_0_1_noPBC_simulation2.xtc -m rmsd-matrix.xpm Selected '4' for back bone atoms. This

Re: [gmx-users] g_cluster

Dear Nikolai, Group 1. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se On 24 Aug 2017, at

[gmx-users] g_cluster

Dear All, I am using g_cluster. I am wondering what two groups used for? group 1 for fit and RMSD calculation group 2 for output is g_cluster use RMSD values for clustering based on group 1 or group 2? Any suggestions? Thanks Nikolai -- Gromacs Users mailing list * Please search the

Re: [gmx-users] g_cluster and g_hbond calculation on GPU

Hi, Please don't re-post the same questions from different emails. You already got the answer that no analysis tools have been ported to run on GPUs. Mark On Wed, Aug 9, 2017 at 3:04 PM Kishwar Hayat Khan wrote: > Hi Everyone, > I would like to run g_cluster and g_hbond

[gmx-users] g_cluster and g_hbond calculation on GPU

Hi Everyone, I would like to run g_cluster and g_hbond calculation on GPU boards. I could only find -nthreads option to fasten my calculations, Is it possible to use GPU boards for this like mdrun. reg Kish -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] g_cluster or g_clustsize

On 7/29/16 1:19 AM, Seera Suryanarayana wrote: Dear Gromacs Users, I would like to do clustering of my trajectories. When I look into gromacs tool for clustering, I got g_cluster which is based on the RMSD and the other one is g_clustsize which computes the size distributions of

[gmx-users] g_cluster or g_clustsize

Dear Gromacs Users, I would like to do clustering of my trajectories. When I look into gromacs tool for clustering, I got g_cluster which is based on the RMSD and the other one is g_clustsize which computes the size distributions of molecular/atomic clusters in the gas phase. Mine is protein in

Re: [gmx-users] g_cluster analysis

Hi Sapna, How should we know how many clusters you should have? A cutoff of 0.2 is quite tight, and will give many clusters. Whether that's what you want/need or whether that's meaningful/helpful for your goals is something you should consider. We don't know what you're trying or doing. Cheers,

[gmx-users] g_cluster analysis

Dear all, I am trying to use g_cluster protocol to get representative snapshots of the simulations. I have concatenated 9 set of simulations and run g_cluster for the same. The result shows a total of 198 clusters. Is this correct? Following is the command I have used: g_cluster -s models.gro

[gmx-users] g_cluster

Hi all, I'm trying to perform a cluster analysis on my MD simulation using g_cluster. I'm analysing a simulation of a 11 base pair DNA sequence 10 ns long with 5000 frames. I have no problem using the program, i runs perfectly using the 'gromos' method. I have 2 questions, one of which is more

Re: [gmx-users] g_cluster (gromos method) creates clusters with members having RMSD greater than the cutoff to the cluster middle

-users-boun...@maillist.sys.kth.se on behalf of Christopher Neale chris.ne...@alum.utoronto.ca Sent: 12 February 2015 22:53 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] g_cluster (gromos method) creates clusters with members having RMSD greater than the cutoff

Re: [gmx-users] g_cluster (gromos method) creates clusters with members having RMSD greater than the cutoff to the cluster middle

...@alum.utoronto.ca Sent: 12 February 2015 22:53 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] g_cluster (gromos method) creates clusters with members having RMSD greater than the cutoff to the cluster middle Dear Users: I have run g_cluster from gromacs 4.6.5 as follows

[gmx-users] g_cluster (gromos method) creates clusters with members having RMSD greater than the cutoff to the cluster middle

Dear Users: I have run g_cluster from gromacs 4.6.5 as follows: g_cluster -s my.tpr -f tmp.xtc -method gromos -nofit -o rmsd-clust_nofit.xpm -g cluster_nofit.log -sz clust-size_nofit.xvg -cl clusters_nofit.pdb -n index.ndx -cutoff 0.275 -wcl 10 -cl finally.xtc The top of cluster_nofit.log

[gmx-users] g_cluster and loops dynamics

Dear Gromacs Users! I'd like to cluster ensemble of the conformations of the long (30 aa) loop using g_cluster method and one of its clustering methods based on the RMSD cut-off. Briefly during the md run I've observed different secondary structure elements formations within the loop- so I'd like

Re: [gmx-users] g_cluster analysis for structure refirement

Thanks! That was very usefull. BTW have someone tried some software for visualization of such clusters and compution of the percents of the SS elements in each cluster (for instance by comparison of the most representative structures from each cluster etc). Might this VMD plugin

Re: [gmx-users] g_cluster analysis for structure refirement

Hi Tsjerk, thanks for suggestions! Some additional questions regarding g_cluster method. 1- how most correctly select cutoff value for clustering of the surface-exposed loops assuming big number of clusters? In literature I've found cutoff ~ 1.3 A for enzymes active-site loops applicable for

[gmx-users] g_cluster analysis for structure refirement

Dear Gromacs users! I'd like to use g_cluster utility to cluster a big set of models produced by Modeller as the result of the refirement of some parts of my protein. In this case all structures differs only in the conformation of 1 longest loop (~ 30 amino acids including 2 disulphide bridges)

Re: [gmx-users] g_cluster analysis for structure refirement

Hi James, The first part is just conformational clustering, for which you can use g_cluster. The easiest is then to collect the structures belonging to the different clusters in different files (which g_cluster can do), which you process separately to extract those properties you're interested

[gmx-users] g_cluster for ligand clustering

Dear all, I have a trajectory file of a protein+ligand binding simulation. What I would like to do is to cluster the ligands positions from the simulation trajectory. But although I have tried quite a few possibilities, the RMSD calculation using g_cluster will change the reference

[gmx-users] g_cluster

Hi List, I have come across mailing list where g_cluster can possibly be used for clustering of docked ligands. I tried g_cluster but it will change the reference coordinates with respect to the receptor. Is there a way to do clustering using g_cluster based on binding site? Many thanks, Neha

Re: [gmx-users] g_cluster: treating identical molecules as interchangeable

Hi, I would expect there is no way to do this with g_cluster. g_cluster -h should mention it if it did exist. The only way to implement it is to iterate over all permutations of equivalent molecules. That's doable, but it would have to have been implemented deliberately. Mark On Tue, May 13,

[gmx-users] g_cluster failing

Hello GMX users, I hope you could help me solving this un-understandable (at least for me) error. I am trying to run g_cluster on one of my collected trajectories using the following command g_cluster -f allnj_1.xtc -n index.ndx -o -g -dist -ev -sz -tr -ntr -clid -cl -cutoff 0.5 -skip 10 -s

Re: [gmx-users] g_cluster failing

Building all-against-all matrices takes a lot of memory, and if it runs out, then crazy things happen. I suggest you start with versions of your trajectories sampled very sparsely so there are few tens of samples, and get a sane result from g_cluster from that. Then scale up / find a lot of memory

Re: [gmx-users] g_cluster

Sarcasm perceptivity deficiency is a socially crippling disorder which renders the sufferer oblivious to sarcasm and leads him to treat sarcastic remarks as if they were sincere. Cheers, João On Fri, Feb 7, 2014 at 10:45 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hey Mehmet, If you don't

Re: [gmx-users] g_cluster

Let's make sure we keep it friendly and constructive! :-) Mark On Feb 9, 2014 12:23 PM, João Henriques joao.henriques.32...@gmail.com wrote: Sarcasm perceptivity deficiency is a socially crippling disorder which renders the sufferer oblivious to sarcasm and leads him to treat sarcastic

Re: [gmx-users] g_cluster

My apologies, I didn't mean to offend anyone. It was a mere humoristic attempt to state the obvious, ie. some users are not going to understand mildly sarcastic remarks and that will only help confusing them even more. Yet, I fully understand that my citation was a bit too much for this mailing

Re: [gmx-users] g_cluster

I don`t know about -h but -cl BLAHBLAH.pdb works for sure… you should also provide cutoff (most standard is around 0.3) by -cutoff 0.3 Mehmet -- View this message in context: http://gromacs.5086.x6.nabble.com/g-cluster-tp5014116p5014393.html Sent from the GROMACS Users Forum mailing list

Re: [gmx-users] g_cluster

Hey Mehmet, If you don't know about -h, try it once ;) Cheers, Tsjerk On Fri, Feb 7, 2014 at 10:37 PM, Mehmet Ozbil m.oz...@umiami.edu wrote: I don`t know about -h but -cl BLAHBLAH.pdb works for sure… you should also provide cutoff (most standard is around 0.3) by -cutoff 0.3 Mehmet --