Re: [gmx-users] (no subject)

What is your protein, PDB Id ? FR. > Le 14 mai 2016 à 12:04:09, Upasana Ray <upasanaray...@gmail.com> a écrit : > > yes I have removed water & the pdb file only contains protein > > On Sat, May 14, 2016 at 1:50 PM, Chalaoux, Francois-Regis < > francois-r

Re: [gmx-users] (no subject)

Hi, Did you removed Water ? Check also there is no other protein in the same file. FR. > Le 14 mai 2016 à 07:04:15, Upasana Ray a écrit : > > Dear user, > > I have generated my final protein.pdb file by using trjconv command from > .xtc file. The size of my pdb

[gmx-users] do_dssp strange reaction

Hi everybody, Trying to use do_dssp_mpi for my MD I got an error described below. I gave "-ver 2" for dssp 2.0.4 but nothing changed. This is a real pain in the neck since a week to debug this message. Any tracks Guys ? FRC Config: Linux Centos 6.7 Gromacs mpi 5.04 == CMD and

Re: [gmx-users] How to Compile tools without mpi ?

...@gromacs.org; gromacs.org_gmx-users@maillist.sys.kth.se Objet : Re: [gmx-users] How to Compile tools without mpi ? Hi, Per the install guide, don't use an MPI wrapper compiler, and/or don't use -DGMX_MPI=on cmake option. Mark On Wed, May 4, 2016 at 4:35 PM Chalaoux, Francois-Regis < franc

Re: [gmx-users] How to Compile tools without mpi ?

e tools without mpi ? >> >> Hi, >> >> Per the install guide, don't use an MPI wrapper compiler, and/or don't use >> -DGMX_MPI=on cmake option. >> >> Mark >> >> On Wed, May 4, 2016 at 4:35 PM Chalaoux, Francois-Regis < >> francois-re

[gmx-users] How to Compile tools without mpi ?

Hi, How to compile tools without mpi (i.e. do_dssp) ? FR -- 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

Re: [gmx-users] GROMACS 5.1.4 released

Hi All, What are the differences between" Gromacs 2016" and" Gromacs 5.1.4" ? Cheers, FR. François-Régis Chalaoux Drug Design, EVOTEC Toulouse De : gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se]

Re: [gmx-users] GROMACS 5.1.4 released

leased Hi, All releases come with notes about what has changed - see http://manual.gromacs.org/documentation/2016/ReleaseNotes/. From 5.1 to 5.1.4 only bugs got fixed, and you can read about them for each such version. Mark On Wed, Sep 14, 2016 at 3:38 PM Chalaoux, Francois-Regis < francoi

Re: [gmx-users] GROMACS 5.1.4 released

romacs.org; gromacs.org_gmx-users@maillist.sys.kth.se Objet : Re: [gmx-users] GROMACS 5.1.4 released Hi, Yes... From the first sentence of my link "These release notes document the functionality changes that have taken place in GROMACS since version 5.1" Mark On Thu, 15 Sep 2016 09:06 Chal

Re: [gmx-users] Align a vector with an axis of the box

r 23, 2017 at 3:25 PM Chalaoux, Francois-Regis < francois-regis.chala...@evotec.com> wrote: > Hi All, > > To realize an umbrella sampling of JZ4 in the Lyzosyme (3HTB) I have > to define a box enough long to pull JZ4. I choose a reaction > coordinate between Calpha

[gmx-users] Align a vector with an axis of the box

Hi All, To realize an umbrella sampling of JZ4 in the Lyzosyme (3HTB) I have to define a box enough long to pull JZ4. I choose a reaction coordinate between Calpha THR109 and JZ4-COM. Presently, this coordinate (vector) is not aligned with an axis of my cubic box and after a pulling should

[gmx-users] Align a vector with an axis of the box

Hi All, To realize an umbrella sampling of JZ4 in the Lyzosyme (3HTB) I have to define a box enough long to pull JZ4. I choose a reaction coordinate between Calpha THR109 and JZ4-COM. Presently, this coordinate (vector) is not aligned with an axis of my cubic box and after a pulling should