[gmx-users] pullx (gromacs 4.6 vs 2016)

[gromacs query]

Hi All,

Am just wondering if somebody has seen this in different gmx versions?

Thanks.
JIom


On Fri, Aug 25, 2017 at 11:00 AM, gromacs query <gromacsquery at gmail.com>
wrote:

> Hi All,
>
> I am using 'equivalent' mdp settings for pull run in Gromacs 4.6 and 2016.
>
> With gromacs 4.6 I get time, 0Z and 1dZ; which I can understand as
> explained here:  https://www.mail-archive.com/g
> mx-users at gromacs.org/msg22453.html
>
> With Gromacs 2016 I get only time and some distance and xvg file says is
> Position. Is it same as 1dZ? Just wondering why 0Z is not printed.
>
> #####> pull settings for 4.6<####
>
> pull            = umbrella
> pull_geometry   = direction ;
> pull-vec1 = 0 0 -1
> pull_dim        = N N Y ;
> pull_start      = yes       ; define initial COM distance > 0
> pull_ngroups    = 1
> pull_group0     = Mem ; restrained group
> pull_group1     = Peptide; group to pull
> pull_init1 = 0
> pull_rate1      = 0.0; nm per ps
> pull_k1         = 1000       ; kJ mol^-1 nm^-2
> pull-nstxout = 1000;
> pull-nstfout = 1000;
> ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
>
>
> #####> pull settings for 2016<####
>
> pull = yes
> pull_coord1_type        = umbrella ; equivalent to  pull = umbrella
> pull_coord1_geometry    = direction   ; equivalent to pull_geometry   =
> direction ;
> pull-coord1-vec         = 0 0 -1      ; equivalent to pull-vec1 = 0 0 -1
> pull_coord1_dim      = N N Y       ; equivalent to pull_dim = N N Y ;
> pull_coord1_start     = yes; equivalent to pull_start  = yes ; define
> initial COM distance > 0
> pull_ngroups            = 2           ; equivalent to pull_ngroups    = 1
> pull_coord1_groups      = 1 2
> pull_group1_name        = Mem           ; equivalent to  pull_group0
> pull_group2_name        = Peptide             ; equivalent to
> pull_group1
> pull-coord1-init        = 0           ;  pull_init1 = 0
> pull_coord1_rate        = 0.00000           ; equivalent to pull_rate1
> pull_coord1_k           = 1000           ; equivalent to pull_k1         =
> 1000       ; kJ mol^-1 nm^-2
>
>
> Thanks
>
> JIom
>