[gmx-users] Umbrella sampling - Pull distance is larger than 0.49 times box size error

金 瑞涛 jinruitao at hotmail.com
Sat Jan 27 15:05:25 CET 2018


Have you tried different pressure coupling type? Maybe a semi-isotropic one will solve the problem if you chose z-axis as your pulling vector direction.

Best regards


Sent from my Samsung Galaxy smartphone.

-------- Original message --------
From: Shrinath Kumar <shrinath.kumar at ucdconnect.ie>
Date: 28/1/18 12:53 am (GMT+10:00)
To: gmx-users at gromacs.org
Subject: [gmx-users] Umbrella sampling - Pull distance is larger than 0.49 times box size error


I'm doing umbrella sampling and running into the above error. I can't
really increase the box size as that would make the system too big nor can
I use pull-geometry = direction-periodic as I need to use NPT.

But I'm confused on why I get this error in the first place because my
periodic box is a cuboid and the pulling distance is less than 0.5*box size
in each dimension. So the pulling vector should be uniquely determined and
there should be no discontinuities.

To solve this I tried having 3 pull coordinates each acting on a separate
dimension. This solves the grompp error. But would this produce the same
results as having 1 pull coordinate acting on all 3 dimensions? Or is there
any better workaround for this?

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 visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list