Re: [gmx-users] calculate angle between two beeta sheet

First define the two vectors e.g. select the c-alphas of residues 43 and 45 (vector1) and residues 51 and 53 (vector2). Then calculate the angle between the two vectors (possibly using the command g_sgangle). This will give you a time series of the angle between the two above-mentioned vectors.A

Re: [gmx-users] calculate angle between two beeta sheet

can anyone please help me in this regards. On 1/4/19, SHAHEE ISLAM wrote: > hi, > my protein contain three beeta sheet. > (i) resid 43-45 > (ii) resid 51-53 > (iii) resid 58-59 > i want to calculate the angle between two beeta sheet.can any one > please suggest me how i can do this. > thanking yo

[gmx-users] inflategro2

Hi All, My membrane contains a mixture of DPPC and DOPC lipids and aligned protein. I am trying to insert protein into the membrane using inflategro2 scripts. During the running the script is writing: Deep recursion on subroutine "main::dynInflating" at /home/gnss/netaly/FL_CFTR_Cduction/onelayer/

Re: [gmx-users] Selections in gromacs

Hi, If it's the same two molecules each time, then you can use a static index group. Is it? Mark On Sun, Jan 6, 2019 at 8:41 PM Tuanan Lourenço wrote: > Hi everyone, > > I am trying to use the "gmx trjconv" to write a new trajectory from my > "main trajecetory" that contains just two molecules

[gmx-users] Selections in gromacs

Hi everyone, I am trying to use the "gmx trjconv" to write a new trajectory from my "main trajecetory" that contains just two molecules then they are close to each other in a specific distance. The idea is to have a new trajectory that contains these molecules in this specific distance in each fra

Re: [gmx-users] gmx hbond

Thank you. But it just adjusts the cut-off between atoms not the number of hydrogen bonds in a given distance above the surface (or in the box). would you please help me? Best On Sun, Jan 6, 2019 at 9:12 PM paul buscemi wrote: > Use VMD/extensions/hydrogen bonds > > > On Jan 6, 2019, at 11:01 A

Re: [gmx-users] gmx hbond

Use VMD/extensions/hydrogen bonds > On Jan 6, 2019, at 11:01 AM, rose rahmani wrote: > > hi, > > I want to know the number of hydrogen bonds of amino acid with water in > different distances above surface. for example in first 0.2nm, in second > 0.2 nm(0.2-0.4 nm) above surface. how can i do it

[gmx-users] gmx hbond

hi, I want to know the number of hydrogen bonds of amino acid with water in different distances above surface. for example in first 0.2nm, in second 0.2 nm(0.2-0.4 nm) above surface. how can i do it by gmx hbond? I couldn't find any proper option for that. best -- Gromacs Users mailing list * P

[gmx-users] inflategro2

Hi All, My membrane contains a mixture of DPPC and DOPC lipids and aligned protein. I am trying to insert protein into the membrane using inflategro2 scripts. During the running the script is writing: Deep recursion on subroutine "main::dynInflating" at /home/gnss/netaly/FL_CFTR_Cduction/onelayer/

Re: [gmx-users] AMD 32 core TR

It also comes into my mind that the AMD 32 core has not a double performance of AMD 16 core. Because of manufacturing the 4 dies (4x8 cpu units), it does not have the same bandwidth to the RAM. But this is told to affect only memory hungry applications. Thus at this moment I think that this doe

Re: [gmx-users] AMD 32 core TR

Paul, I agree with Mark, since most likely the cause of the small increase in performance is because the workload of the CPU and GPU. In your case the performance is limited by the GPU. It likely runs at 100% with 8CPU. Then adding extra CPUs does not help. I am experiencing with 16 CPUs (2