Re: [gmx-users] How many times should I do Umbrella Sampling

Hi Agnivo, In addition to the remarks of Andre, if you can show that another US run on the same system gives pretty much the same result, then you can present that as proof of the robustness, and it is futile to do three more, especially if you have convergence and sufficient overlap. You can

Re: [gmx-users] gmx hbond - specify precise atom names involved

Hi, Not as of yet I’m afraid. Erik > On 3 May 2016, at 08:16, Nash, Anthony wrote: > > > Hi all, > > Can gmx hbond accept user specified atoms for the donors (default OH and > NH) and acceptor (default O and N)? I don¹t seem to find any mention of > this in the -help text.

[gmx-users] installation error gromacs-imd

Dear gromacs users i was trying to install gromacs-imd that was developed by Martin Hoefling http://www.mpibpc.mpg.de/grubmueller/interactivemd all configuration is ok with this command: CC=$HOME/software/openmpi/bin/mpicc CXX=$HOME/software/openmpi/bin/mpicxx

[gmx-users] Empty output files from gmx helix?

Hi everyone, I have a 21-mer peptide A for helix analysis using gmx helix in GROMACS 5. When I select residues 3-19 when executing gmx helix, everything looks fine. But when I select another set of residues, e.g. 8-19, the output len-ahx.xvg file ends after: # This file was created Thu Jun 9

Re: [gmx-users] How many times should I do Umbrella Sampling

Hi Agnivo, good overlap of histograms and a smooth pmf cannot be taken as evidences of convergence. Some people would extend the simulations to prove that pmf does not change appreciably with further sampling, while other people (as your reviewer) would do extra independent pmf profiles to prove

[gmx-users] frame with lowest energy

hello gromacs users and experts, i have performed 10ns complex simulation of Protein and ligand-complex, now i need the best conformation for further analysis (alchemical analysis: binding free energy simulations). i want to choose best initial structure for further study. how would i know

[gmx-users] How many times should I do Umbrella Sampling

Hello Users I did one umbrella sampling on a trajectory generated by a pulling simulation. There were 45 windows in my US and the PMF curve converged with good overlap of histograms. However the reviewer is asking for 5 US simulations from 5 pulling sims on the same system and wants the average

Re: [gmx-users] Calculating avergae structure from the simulation

gmx rmsf -f *.xtc -s *.tpr -o rmsf-per-residue.xvg -ox average.pdb -oq bfactors.pdb -res This would give you a average structure. On Wed, Jun 8, 2016 at 5:21 PM, Agnivo Gosai wrote: > Dear Users > > I had run an unrestrained 50 ns simulation of a protein-ligand

Re: [gmx-users] Calculating avergae structure from the simulation

On 6/8/16 5:21 PM, Agnivo Gosai wrote: Dear Users I had run an unrestrained 50 ns simulation of a protein-ligand complex using GROMACS to check the stability of the force field used and compare with previous literaure. Then I dumped the strucuture from the last frame of the 50 ns simulation

Re: [gmx-users] making topology file manually

On 6/8/16 10:49 AM, Mohsen Ramezanpour wrote: Thanks Justin, This is why I have got confused then, as each force field treats them in a different way. Knowing the details of force field seems necessary then. As another solution to this: Can we just make the topology file using some web

Re: [gmx-users] Constant-velocity pulling

On 6/8/16 9:51 AM, Sajjad Kavyani wrote: Dear experts, I'm trying to do a constant-velocity pulling of water particles through a tube. First, I did the process with a constant force constant successfully but now for the constant velocity, I do not get how to choose parameters in the .mdp

Re: [gmx-users] Domain Decomposition does not support simple neighbor searching.

On 6/8/16 9:41 AM, Daniele Veclani wrote: Dear Gromacs Users I'm trying to do a simulation in a NVE ensemble in vaccum. But I but I find this error: "Domain Decomposition does not support simple neighbor searching, use grid searching or run with one MPI rank" If I use ns_type=grid I can

[gmx-users] Calculating avergae structure from the simulation

Dear Users I had run an unrestrained 50 ns simulation of a protein-ligand complex using GROMACS to check the stability of the force field used and compare with previous literaure. Then I dumped the strucuture from the last frame of the 50 ns simulation and used it for pulling and umbrella

Re: [gmx-users] Saving time of the coordinates for conformational entropy

Hi Qasim, The RMSD is not good for assessing convergence, especially if it goes above 0.5 nm. Cheers, Tsjerk On Wed, Jun 8, 2016 at 8:48 PM, Qasim Pars wrote: > Dear users, > > I have simulated a protein with simulation time of 200 ns and saving the > coordinates at

Re: [gmx-users] PCA problems

On Wed, 8 Jun 2016, Tsjerk Wassenaar wrote: Hey :) That usually gives a fitted ensemble that more closely retains the original RMSD values between all pairs of structures. This should read: ... a fitted ensemble of which the sum of the traces of all pairwise inner product matrices is

Re: [gmx-users] PCA problems

Hey :) > That usually gives a fitted ensemble that more closely retains the > original RMSD values between all pairs of structures. > This should read: ... a fitted ensemble of which the sum of the traces of all pairwise inner product matrices is closer to minimal. The pairwise RMSDs (and

Re: [gmx-users] PCA problems

Hi James, If your molecule shows some flexiblility, I would suggest using as a reference the structure of your original ensemble that produces the fitted ensemble with the lowest sum of RMSD values to that structure (or their square). That usually gives a fitted ensemble that more closely

[gmx-users] Saving time of the coordinates for conformational entropy

Dear users, I have simulated a protein with simulation time of 200 ns and saving the coordinates at every 40 ps. Conformational entropy (~4500 kJ/mol K) obtained by Quasiharmonic approach using gmx covar and gmx anaeig tools is not consistent with literature (~2500 kJ/mol K). Whereas, the RMSD

Re: [gmx-users] PCA problems

ok thanks Tsjerk. I think that makes sense now. Best wishes James > Hi James, > > That's silly! Ambiguous means that the same structure can have multiple > solutions in a fit. The fit to a single reference structure (with more > than > three atoms) is never ambiguous. Can never, by definition! >

Re: [gmx-users] PCA problems

In addition to what Tsjerk said, may I point out that a publication by a colleague of mine treats exactly these problems that arise when trying to fit cartesian structures: http://scitation.aip.org/content/aip/journal/jcp/141/1/10.1063/1.4885338 Regards, Matthias On 06/08/2016 06:10 PM, Tsjerk

Re: [gmx-users] PCA problems

Hi James, That's silly! Ambiguous means that the same structure can have multiple solutions in a fit. The fit to a single reference structure (with more than three atoms) is never ambiguous. Can never, by definition! Now if you have two reference structures at hand, and they have (quite)

Re: [gmx-users] PCA problems

Thanks Tsjerk, Isn't the progressive fit supposed to rotate everything back into the same orientation without having to worry about inferring that orientation from a reference structure that doesn't align well? Each configuration should in theory align well to its predecessor all the way back to

Re: [gmx-users] making topology file manually

Thanks Justin, This is why I have got confused then, as each force field treats them in a different way. Knowing the details of force field seems necessary then. As another solution to this: Can we just make the topology file using some web servers or software (ATB, SwissParam, Antechamber,

[gmx-users] g_helixorient

Hello, I have been working with some dimer protein molecule, on gromacs, trying to analyze the structure of the dimer, and how the monomers orient according to eachother. The monomer is an alpha-helix, having 36 residues. I wanted to calculate the rho angle for some residues in my helical

Re: [gmx-users] RMSD question

Hi Teresa, You probably want to try clustering, and then check the percentage of bound/unbound structures in the clusters you get. Just the RMSD won't tell you much. Cheers, Tsjerk On Wed, Jun 8, 2016 at 11:30 AM, ingram wrote: > Dear GROMACS community, > > I am

Re: [gmx-users] PCA problems

Hi James, 'Spurious alignment' is the dependence of the resulting ensemble on the reference structure. Unfortunately, that's not solved by a progressive fit. Rather, in a progressive fit, the same configuration can have multiple orientations, based on the previous structures, which is also

[gmx-users] Constant-velocity pulling

Dear experts, I'm trying to do a constant-velocity pulling of water particles through a tube. First, I did the process with a constant force constant successfully but now for the constant velocity, I do not get how to choose parameters in the .mdp file!. I read the umbrella sampling tutorial,

[gmx-users] Domain Decomposition does not support simple neighbor searching.

Dear Gromacs Users I'm trying to do a simulation in a NVE ensemble in vaccum. But I but I find this error: "Domain Decomposition does not support simple neighbor searching, use grid searching or run with one MPI rank" If I use ns_type=grid I can generate the .tpr file, But when I run mdrun I

[gmx-users] RMSD question

Dear GROMACS community, I am trying to identify the number of unique peptide structures on the surface of a slab. If I simply calculate the RMSD between the protein atoms in each frame of the trajectory this tells me nothing about how these structures compare on the surface as the constraint

Re: [gmx-users] interpreting the output of gmx tune_pme

Hi, > On 07 Jun 2016, at 22:00, jing liang wrote: > > Hi, > > the output of "gmx tune_pme" in perf.out file reports the following line at > the end: > > Line tpr PME ranks Gcycles Av. Std.dev. ns/dayPME/f > DD grid > > how can I interprete

Re: [gmx-users] PCA problems

Thanks very much for your help. I have tried with a .tpr file and there is an improvement but still breaks. Similarly when I apply the same protocol as I said previously, but with my peptide unbound I get the same problem however in this case the free peptide has no pbc conditions Best

Re: [gmx-users] itp or top parameters for HEM?

Hi, there is a paper from Ulucan et al: Energetics of hydrophilic protein-protein association and the role of water (http://pubs.acs.org/doi/abs/10.1021/ct5001796?journalCode=jctcce=10=3512=citation=10) In the supporting info you can find HEME params they used for an amber ff. I hope that

Re: [gmx-users] PCA problems

Dear Teresa, That sounds like a periodic boundary issue to me. It could be fixed by using a tpr instead of a gro as the gmx covar manual says "All structures are fitted to the structure in the structure file. When this is not a run input file periodicity will not be taken into account."

Re: [gmx-users] PCA problems

Hi Teresa, No, the peptide should not be broken. Did you remove jumps over PBC? The peptide will probably be severely distorted by filtering, though. Cheers, Tsjerk On Wed, Jun 8, 2016 at 8:49 AM, ingram wrote: > Dear GROMACS community > > I am trying to complete a

[gmx-users] PCA problems

Dear GROMACS community I am trying to complete a PCA analysis of my peptide adsorbed to a surface. However when I use : gmx covar -s trajectory.gro -f md_golp_vacuo.xtc and select the protein for both the least squares fit and covariance calculation, followed by gmx anaeig -s

Re: [gmx-users] distance between two groups

To calculate the distances from your ligand to multiple residues, a much better way than a loop over multiple gmx distance calls would be to use gmx pairdist, which should be able to calculate the distances you want in one go. Teemu On Wed, Jun 8, 2016, 03:35 Justin Lemkul