Re: [gmx-users] Query regarding do_dssp program

totally different secondary structures that's why I was worrying.. because these are major structures one reports so Very important to resolve this issue. On Wednesday, January 15, 2020, Justin Lemkul wrote: > > > On 1/13/20 9:15 AM, Sundari wrote: > >> Yes, Sir, I made the gro fil

Re: [gmx-users] Query regarding do_dssp program

sp shows 8 residues making beta-sheets but when I load that particular time frame in vmd for visualizing the structure, these 8 residues showing 5-helix structure. Please suggest something. On Mon, Jan 13, 2020 at 7:01 PM Justin Lemkul wrote: > > > On 1/13/20 7:22 AM, Sundari wr

Re: [gmx-users] Query regarding do_dssp program

s any way to animate secondary structure in vmd according to dssp algorithm. Best regards, Sundari On Mon, Jan 13, 2020 at 1:37 PM Alessandra Villa < alessandra.villa.bio...@gmail.com> wrote: > Hi, > VMD and dssp may use a slightly different criteria to define a beta > sheet.

[gmx-users] Query regarding do_dssp program

Dear Gromacs Users, I have a big query regarding the "do_dssp" tool of gromacs-5.1.2. Whenever I calculate the protein secondary structure by "gmx do_dssp" , it shows a significant amount of beta sheet structures. But when I load the same trajectory file in VMD for visualization of the secondary

[gmx-users] Doubt in nmol tool

Dear Gromacs users, Can anyone explain about -nmol (number of molecules ) option in gmx gyrate tool. According to me I have 3 peptide chains in my simulation box and I am using " -nmol 3". Is it correct what I have used for this option? Regards Sundari -- Gromacs Users mailing list

Re: [gmx-users] Regarding MM/GBSA method implemented in the GROMACS package

idea. sundari On Fri, Sep 28, 2018 at 8:47 PM rose rahmani wrote: > Hi, > > You can calculate adsorption energy by umbrella sampling. > http://www.mdtutorials.com/gmx/umbrella/index.html > .edr just gives you the interaction energy not adsorption energy and > distance. > &

[gmx-users] Regarding MM/GBSA method implemented in the GROMACS package

can get these binding energies. Regards, Sundari -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https

[gmx-users] Regarding MM/GBSA method implemented in the GROMACS package

Dear Gromacs users, I want to calculate Binding energy between the protein and the carbon nano tube. Is there any way to do that by gromacs commands. As I only have .xtc and .tpr files from gromacs. Please suggest me any idea or any article so that based on trajectories (xtc or trr) how one

Re: [gmx-users] Increase of 5-helix count

Kindly look at my query.. Thank you! On Mon, Jun 11, 2018 at 5:39 PM, Sundari wrote: > Dear gromacs users, > > I am running a simulation of three alpha helical peptides with a carbon > nano tube in a simulation box. Actually I am following a paper and want to > reproduce the res

[gmx-users] Increase of 5-helix count

Dear gromacs users, I am running a simulation of three alpha helical peptides with a carbon nano tube in a simulation box. Actually I am following a paper and want to reproduce the results. In my simulation every time there is a sudden increase of 5-helix count, means most of the alpha helix

Re: [gmx-users] REMD temperature_space

Hello Guys, Kindly suggest me something about my doubt. On Thu, May 3, 2018 at 5:19 PM, Sundari <sundi6...@gmail.com> wrote: > Hello, > > I got the continuous trajectories by using demux. But now I am confused in > getting potential energy distribution of a single repli

Re: [gmx-users] REMD temperature_space

x script. > > Mark > > On Thu, May 3, 2018 at 1:28 PM Sundari <sundi6...@gmail.com> wrote: > > > Dear gromacs users, > > > > can anyone please suggest me that how we get the time evolution of a > > replica (say replica_1) in temperature space and time course

[gmx-users] REMD temperature_space

replica_index.xvg and replica_temp.xvg. But I want to analyse a single replica trajectory in all temperatures ( temp. on y-axis) Thank you in advance.. Sundari -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting

Re: [gmx-users] Secondary structure propensity.

Thanks a lot ... On Sun, Feb 18, 2018 at 9:19 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 2/18/18 6:05 AM, Sundari wrote: > >> Thank You :) >> >> I have a little doubt now. If I want total percentage of all 8 secondary >> structures separatel

Re: [gmx-users] Secondary structure propensity.

dues in a given secondary structure as a function of time. From that, > percentage over time is a trivial scripting task, [(# in SS) / (# of > residues)]*100. > > -Justin > > Regards, >> >> S. Borkotoky >> >> On Fri, Feb 16, 2018 at 1:30 PM, Sundari

Re: [gmx-users] SS Content?

my problem resolved :) Thank you On Sun, Feb 18, 2018 at 4:22 PM, Sundari <sundi6...@gmail.com> wrote: > Dear gromacs users, > > can any one please tell me that how we get the secondary structure > propensity or secondary structure content(%) as a function of simulation >

[gmx-users] (no subject)

Dear gromacs users, can any one please tell me that how we get the secondary structure propensity or secondary structure content(%) as a function of simulation time. I used "gmx do_dssp" but it gives me number of residues forming the secondary structure vs simulation time. is it same thing or

[gmx-users] Secondary structure propensity.

Dear gromacs users, can any one please tell me that how we get the secondary structure propensity or secondary structure content(%) as a function of simulation time. I used "gmx do_dssp" but it gives me number of residues forming the secondary structure vs simulation time. is it same thing or

[gmx-users] Structures after Dihedral principle component analysis(dPCA)

Dear all I have plotted the Free Energy Landscapes(2D) of proteins from First two principal components as used by GROMACS, But after that I am confused how to do clustering on PCA surface or I want to know how to calculate the structure of protein corresponding to lowest free energy in FELs. Is

[gmx-users] problem with NPT simulation

Dear all, I am doing a protein simulation. After NVT equilibration, I tried to do NPT but everytime I got this error :- --- Program gmx grompp, VERSION 5.1.2 Source code file:

Re: [gmx-users] Secondary structure content

residues, from >>> which computing percentage is trivial based on the number of total >>> residues. >>> >>> -Justin >>> >>> Hope that makes sense. >>> >>>> === >>>> Micholas Dean Smith, PhD. >

[gmx-users] Secondary structure content

Dear all, I am confused with 'dssp' output graph i.e "number of residues vs time". Is it also called "secondary structure content(%) vs time" ?? Or it is different term? please, anyone help me to solve this confusion or send me any link contained proper definition of these two. Thanks in

Re: [gmx-users] Number of Contacts

If anyone have Idea. kindly suggest. On Wednesday, June 28, 2017, Sundari <sundi6...@gmail.com> wrote: > Hi, > > I used the following command.. > gmx mindist -f ../traj_comp3.xtc -s ../md3.tpr -n index.ndx -od > minidist.xvg -on numb_count -d 0.65 > By doing this I

Re: [gmx-users] Number of Contacts

FROc2s here, output is a size.xvg file which is looking something feasible. I am not sure is that output contains number of inter peptide contacts which I needed or this is something else as the name suggested "size.xvg". Please clear my confusion. Thank you! Sundari On Wed, Jun 28,

[gmx-users] Number of Contacts

but i got wrong results. Please suggest me right command line to do this analysis. Thank you! Sundari -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support