[gmx-users] Upgrading to Gromacs/5.1 - Problems with Umbrella Sampling

[Dan Gil]

Hi,

The pullx.xvg file is returning the coordinates of the solvent, and not the
solute (a_Cooh) as I want.
The solute is being pulled in a coordinate other than Z, although I specify:
 pull-coord1-dim =N N Y
What is going on here?

On Sun, Aug 7, 2016 at 7:20 AM, Billy Williams-Noonan <
billy.williams-noonan at monash.edu> wrote:

> Hi All,
>
> I'm having a similar problem and wouldn't mind some advice either.  I am
> getting LINCS warnings on one cluster that I run my sampling on, but the
> pull-code works fine on other clusters we have access to, which is making
> me doubt the entire process.
>
> Best regards,
>
> Billy
>
> On 7 August 2016 at 03:34, Dan Gil <dgilgmx at gmail.com> wrote:
>
> > Hi,
> >
> > I am changing from Gromacs/4.6 to Gromacs/5.1, and I have a piece of .mdp
> > file that I am confused with.
> >
> > I am pulling an atom of solute, indexed a_Cooh, towards the COM of
> solvent.
> > This is a slab geometry, with the plane normal to the z-axis direction.
> My
> > output (pullx.xvg) should contain the deltaZ value between the solute Z
> > coordinate and solvent COM z coordinate. With my current Gromacs/5.1
> > attempt, I don't think I am getting the correct results.
> >
> > On Gromacs/4.6:
> > pull =umbrella
> > pull_geometry =distance
> > pull_dim =N N Y
> > pull_init1 =0
> > pull_k1 =100
> > pull_nstxout =100
> > pull_group0 =SOL
> > pull_group1 =a_Cooh
> >
> > My attempt with Gromacs/5.1:
> > pull =yes
> > pull-ngroups        = 2
> > pull-ncoords        = 1
> > pull-group1-name = a_Cooh
> > pull-group2-name = SOL
> > pull-coord1-type  = umbrella
> > pull-coord1-geometry =distance
> > pull-coord1-groups     = 1 2
> > pull-coord1-dim =N N Y
> > pull-coord1-start        = yes
> > pull-coord1-init          =0
> > pull-coord1-k        =1000
> > pull-print-components = yes
> > pull_nstxout =100
> >
> > Best Regards,
> >
> > Dan
> > --
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>
> --
> Billy Noonan*    |    *PhD Student    *|*    Bsci ( *Adv* ), IA Hon
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