[gmx-users] Pull code errors

[Berk Hess]

Yes, this is due to an improvement.
Set the pbcatom (as the error message tries to say) for the pull groups mentioned. The options are described in the mdp section of the manual.

Berk

________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Mark Abraham <mark.j.abraham at gmail.com>
Sent: Sunday, February 24, 2019 6:55 AM
To: gmx-users at gromacs.org
Cc: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: Re: [gmx-users] Pull code errors

Hi,

There have been some improvements to the pull code, but I don't know
offhand whether they apply here. Do consult the 2019 release notes for
clues.

Mark

On Sat., 23 Feb. 2019, 06:11 Ayesha Fatima, <ayeshafatima.69 at gmail.com>
wrote:

> Dear All,
> I am using Gromax 2019 and running an umbrella sampling for two proteins.
> It is a simple pulling simulation. It is giving me the following error
>
>
> ERROR 1 [file md_pull.mdp]:
>   When the maximum distance from a pull group reference atom to other atoms
>   in the group is larger than 0.5 times half the box size a centrally
>   placed atom should be chosen as pbcatom. Pull group 1 is larger than that
>   and does not have a specific atom selected as reference atom.
>
>
> ERROR 2 [file md_pull.mdp]:
>   When the maximum distance from a pull group reference atom to other atoms
>   in the group is larger than 0.5 times half the box size a centrally
>   placed atom should be chosen as pbcatom. Pull group 2 is larger than that
>   and does not have a specific atom selected as reference atom.
>
> Pull group  natoms  pbc atom  distance at start  reference at t=0
>        1      9157      4579
>        2       589      5113       0.300 nm          0.300 nm
> Estimate for the relative computational load of the PME mesh part: 0.14
>
>
> ----------------------------------------------------------------------------------
> Is there anything to be added in the pull code?
>
> Thank you
> Regards
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