Re: [gmx-users] Testing gromacs on IBM POWER8

Hi, On Wed, Sep 2, 2015 at 9:25 PM Fabricio Cannini wrote: > On 27-08-2015 04:17, Mark Abraham wrote: > > Hi, > > > > I have no idea what you're trying to show with these graphs. Your > vertical > > axis of time makes it looks like a 2.5 year old AMD chip is walking all > >

[gmx-users] unable to plot graph using xmgrace

Hi! I tried plotting the potential energy of my molecule using xmgrace. But it gave a warning: Warning: locale not supported by Xlib, locale set to C Xmgrace opened but I could see no plot. I am new to computational biology. I am using gromacs on a mac.Can you please guide as to how I should

Re: [gmx-users] Extracting Trajectory and False Simulation

​The .top file is not useful for mdrun. It needs a .tpr that you create using grompp, as you certainly had to do for the "ideal" simulation you mention. /J​ On Mon, Sep 7, 2015 at 8:36 AM, Rabindra Raj Oliya wrote: > Thank you for your kind suggestions > But how how

Re: [gmx-users] Extracting Trajectory and False Simulation

Thank you for your kind suggestions But how how can I use my alternative topology file in mdrun -rerun? I found no option to include topol.top in the synopsis you mentioned. Rabindra Raj Oliya Original message From: Tsjerk Wassenaar Date: 07/09/2015

Re: [gmx-users] Reliability about Lipid Order Parameters in GROMACS

Thanks a lot to everybody for the answers. I would like to try the patch Justin suggested, however, it is not working today. Do you know if there is any problem with it? http://redmine.gromacs.org/issues/1166 Thanks a lot for all your help. Best wishes, Rebeca. > To: gmx-us...@gromacs.org >

Re: [gmx-users] Extracting Trajectory and False Simulation

Hi Rabindra, You can do an mdrun -rerun with the original trajectory and the alternative topology. Cheers, Tsjerk On Mon, Sep 7, 2015 at 6:32 AM, Rabindra Raj Oliya wrote: > Actually I have two topology files corresponding to ideal and real system. > Initially I have

[gmx-users] RMSD comparison to a different reference structure.

Hi, I was wondering if you would be able to advise me of the best method to compare a mutated and WT structure. I was hoping to perform RMSD analysis for certain regions within a mutation against the same region within the wild type structure. Unfortunately, the atom numbering is likely to

Re: [gmx-users] vacuum simulation vs specific solvent simulation

Dear Tasneem, You need to reduce the time step. You are doing NVE simulations, where energy conservation is a bit tricky. You are also not using constraints, which also implies you need to reduce time step. Probably below 0.5 fs. Or you can turn on constraints. We have successfully used LINCS

Re: [gmx-users] Reliability about Lipid Order Parameters in GROMACS

Thank you very much for your suggestions, Tom. In fact, Ángel and me are collaborating in this work :) We are using AMBER, not CHARMM, this is why we wanted to know if the error about order parameters had been corrected in the new versions of GROMACS. I will try the patch Justin suggested

Re: [gmx-users] RMSD comparison to a different reference structure.

Perfect! Hadn't thought of that! Was hoping to look at side chain fluctuations as well, but I think if I have the c-alpha comparison to WT and then side chain comparison to self, that should work well. Thanks for your help!!! Natalie From:

[gmx-users] xtc file from other software into Gromacs

Dear gromacs user, i done MD using other software and i made xtc file using the tool available in that software.using these files can i do analyse part using gromacs if yes from where should i start . Generally is there any option in gromacs to use the trajectory files made by other softwares?

Re: [gmx-users] tabulated potential - problem

Sorry, I forgot to change the caption.   Gesendet: Montag, 07. September 2015 um 18:14 Uhr Von: "Liz Bell" An: gmx-us...@gromacs.org Betreff: [gmx-users] tabulated potential - problem Dear all,   Is there a possibility to plot the intramolecular energy terms?   3. of

[gmx-users] tabulated potential - problem

Dear all,   Is there a possibility to plot the intramolecular energy terms?   3. of "Diagnosing an Unstable System" of the page   http://www.gromacs.org/Documentation/Terminology/Blowing_Up   sounds as if this is possible. Gmx energy only shows the interaction energys of the energy groups

Re: [gmx-users] xtc file from other software into Gromacs

On 9/7/15 12:02 PM, Nikhil Maroli wrote: Dear gromacs user, i done MD using other software and i made xtc file using the tool available in that software.using these files can i do analyse part using gromacs if yes from where should i start . The manual is a good place to start. Sorry,

Re: [gmx-users] tabulated potential - problem

On 9/7/15 12:14 PM, Liz Bell wrote: Dear all, Is there a possibility to plot the intramolecular energy terms? 3. of "Diagnosing an Unstable System" of the page http://www.gromacs.org/Documentation/Terminology/Blowing_Up sounds as if this is possible. Gmx energy only shows the interaction

[gmx-users] Blowing Up - intramolecular energy terms

Dear all, Is there a possibility to plot the intramolecular energy terms?   3. of "Diagnosing an Unstable System" of the page   http://www.gromacs.org/Documentation/Terminology/Blowing_Up   sounds as if this is possible. Gmx energy only shows the non bonded interaction energys of the

Re: [gmx-users] tabulated potential - problem

  Sorry I did not know how to deal with the fact that I posted my question with a wrong topic.   Thank you for your answer. But I do not really understand what you mean. My topology contains those things like bond, angle and dihedral terms:    [ bonds ] ;ai   aj  bondTyp  n    k   1    2   

Re: [gmx-users] Blowing Up - intramolecular energy terms

Hi, Total bonds and angles are already available in the .log and .edr files. If some component is blowing up, so will the total. Mark On Mon, Sep 7, 2015 at 6:51 PM Liz Bell wrote: > Dear all, > Is there a possibility to plot the intramolecular energy terms? > > 3. of

[gmx-users] Fatal error pdb

Hello: I'm trying to simulate an halothane molecule in water. I download the halothane at pubchem and converted to pdb format using open babel 2.3.2 but when i use pdb2gmx and select OPLS/AA forcefield it appears: Fatal

Re: [gmx-users] Fatal error pdb

On 9/7/15 2:00 PM, Poncho Arvayo Zatarain wrote: Hello: I'm trying to simulate an halothane molecule in water. I download the halothane at pubchem and converted to pdb format using open babel 2.3.2 but when i use

Re: [gmx-users] Reliability about Lipid Order Parameters in GROMACS

Hi Rebeca, I would have thought you might be better, for an all-atom lipid force field, in modifying the CHARMM force field based VMD tcl script. I believe g_order is intended for united-atom lipids and so predicts the positions of the hydrogen atoms based upon an idealised geometry. This

Re: [gmx-users] tabulated potential - problem

On 9/7/15 1:04 PM, Liz Bell wrote: Sorry I did not know how to deal with the fact that I posted my question with a wrong topic. Thank you for your answer. But I do not really understand what you mean. My topology contains those things like bond, angle and dihedral terms: [ bonds ] ;ai aj

[gmx-users] Vacuum versus Water Simulation

Dear Users, Hi. Alanine peptide was simulated in water and in vacuum under NVE ensemble. The magnitude of harmonic components were similar in both simulations (as shown by Fourier transformation). Is this normal? I thought without the damping by water, the vacuum simulation would have a much

Re: [gmx-users] tabulated potential - problem

Thank you very much Justin. I am going to do follow your recommendation and calculate the distance.   Gesendet: Montag, 07. September 2015 um 19:20 Uhr Von: "Justin Lemkul" An: gmx-us...@gromacs.org Betreff: Re: [gmx-users] tabulated potential - problem On 9/7/15 1:04 PM,

Re: [gmx-users] RMSD comparison to a different reference structure.

Hi, How about comparing only C-alphas? As long as you have the same number of residues, that should work. You need to make reduced versions of your tpr and trajectory files. Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Fellow Fulford JRF, Somerville College Department of