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

[Billy Williams-Noonan]

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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