[gmx-users] SMD - Pulling Error in mdrun 0.49 times box size

Alexander Law alexander.law at pg.canterbury.ac.nz
Tue Nov 25 22:16:55 CET 2014

This error occurs because the shortest distance will be used for analysis. There are 2 distances, the linear distance between group 0 and group 1, the other distance passes outside the PBC and enters on the otherside, at the backside of group0. Your box is too small, increase the distance of the length which the force is being applied (Z i e tutorial).
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Agnivo Gosai [agnivogromacs14 at gmail.com]
Sent: Wednesday, November 26, 2014 8:44 AM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] SMD - Pulling Error in mdrun 0.49 times box size

Dear Users

I have put my molecule complex in a box having dimensions 7.5 7.5 15 . The
center of the molecule is fixed as 3.75 3.75 and 4.0.

I use pull geometry = distance.

I did the following SMDs keeping pull force constant unchanged :

1. 500 ps SMD with pull rate = 0.01 nm / ps. mdrun successfully completed.
nsteps = 250000 dt = 0.002

2. 1 ns SMD with pull rate = 0.005 nm / ps. mdrun successfully completed
nsteps = 500000 dt = 0.002

3. 5 ns SMD with pull rate = 0.001 nm / ps. nsteps = 2500000  dt = 0.002 .

Error after the 2383000 th step

Distance of pull group 1 (7.306606 nm ) is larger than 0.49 times the box
size ( 7.455605 ). You might want to consider using "pull-geometry =
direction-periodic" instead.

I also noticed that the "distance at start " for pull group 1 = 2.560 in
grompp output. Initially I thought that this distance plus 5 nm (the total
pulling distance) > 0.49 times 15 nm ( length of box in z direction ) and
is contributing to the error. But this has been the same in cases 1 and 2
also. Hence I am getting confused.

Any suggestions , please ??

Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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