Re: [gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ?

2017-05-26 Thread David van der Spoel
On 26/05/17 22:05, Erik Marklund wrote: “Pairs within 0.35 nm”. They also don’t fulfil the angle criterion, which is why they are sometimes fewer than the hbonds. Therefore I would assume they are more instead. Kind regards, Erik On 26 May 2017, at 19:38, Adarsh V. K.

Re: [gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ?

2017-05-26 Thread Erik Marklund
“Pairs within 0.35 nm”. They also don’t fulfil the angle criterion, which is why they are sometimes fewer than the hbonds. Kind regards, Erik > On 26 May 2017, at 19:38, Adarsh V. K. wrote: > > Dear all, > > The 'gmx hbond' command returns a *.xvg file... viz. "

[gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ?

2017-05-26 Thread Adarsh V. K.
Dear all, The 'gmx hbond' command returns a *.xvg file... viz. " hbnum.xvg " I would like to edit the file before viewing in 'Xmgrace' I opened the hbnum.xvg using 'gedit'. It shows following details (see below) Can you please tell me what is there in the third column of the file?

Re: [gmx-users] RMSF per residue

2017-05-26 Thread Mohsen Ramezanpour
Hi Justin, Here is what I understand. I would like to know if I understood correctly. Given a selection, which has all the heavy atoms (5 atoms) in the side chain of one specific residue (say Lysine), I want to have only "one value" for the average fluctuation of this selection. Thus, I will use

Re: [gmx-users] Perturbation Thermodynamic Integration

2017-05-26 Thread Dan Gil
Hello, I've run Gromacs following the suggestions, but I still get nonzero contributions from the mass changing. I will outline in-depth what I did. Thank you very much for your help! (1) Heptane molecule was inserted into a box of size 10x10x10 nm3 with 7833 water molecules using Gromacs

Re: [gmx-users] RMSF per residue

2017-05-26 Thread Justin Lemkul
On 5/26/17 2:22 AM, Mohsen Ramezanpour wrote: Hi Justin, I have a naive question on tool development for gromacs. If I change part of the code, or if I write a new analysis tool in c++ and add it to this directory (after compiling with g++), shall I still recompile the whole Gromacs again?

Re: [gmx-users] RMSF per residue

2017-05-26 Thread Mohsen Ramezanpour
Hi Justin, I have a naive question on tool development for gromacs. If I change part of the code, or if I write a new analysis tool in c++ and add it to this directory (after compiling with g++), shall I still recompile the whole Gromacs again? Cheers, Mohsen On Thu, May 25, 2017 at 1:43 PM,