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

Agnivo Gosai agnivogromacs14 at gmail.com
Wed Nov 26 00:35:17 CET 2014

Mr. Law

I understand your argument regarding the box length along the Z axis but
for the same box length I did complete 2 successful SMD runs of 500 ps and
1 ns , having different pull rates but in effect the same pulled distance
of 5 nm. Only in the 5 ns SMD , the mdrun crashed with the error as
mentioned in my initial ( trailing ) mail.

My question is , why I need to change box dimension now ? Or may be because
I am simulating under an NPT ensemble , the box vectors had enough time to
change and thus contribute towards the error ?

Please share your suggestions.

---------- Forwarded message ----------
From: Alexander Law <alexander.law at pg.canterbury.ac.nz>
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Date: Tue, 25 Nov 2014 21:16:42 +0000
Subject: Re: [gmx-users] SMD - Pulling Error in mdrun 0.49 times box size
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).
---------- Forwarded message ----------
From: Agnivo Gosai <agnivogromacs14 at gmail.com>
Date: Tue, Nov 25, 2014 at 1:44 PM
Subject: SMD - Pulling Error in mdrun 0.49 times box size
To: gromacs.org_gmx-users at maillist.sys.kth.se

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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