On 8/20/15 6:05 PM, 折晓会 wrote:
Thank you professor Justin! I solved this error which comes from the decimals
of the box dimensions. Initially, my box dimensions are 4.5*4.5*16 nm3 and the
local pressure calculation does not work, but after I change them to be
integers 4*4*16 nm3 in the gro file, the simulation works. It is strange for
me. I do not know why.
I fail to see how making the box smaller solves a "box too small" error, and
moreover, making changes like this is going to affect the results. Don't
consider this a solution. Probably an indication of a bug. So you're just
reading in a .gro file? Does a single coordinate file trigger the error before,
or was that from an actual trajectory?
-Justin
Best wishes,
Xiaohui
Date: Thu, 20 Aug 2015 16:44:58 -0400
From: jalem...@vt.edu
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Incorrect number of parameters - found 3, expected 1
or 1 for Polarization.
On 8/20/15 4:01 PM, 折晓会 wrote:
Thank you professor Justin! I solved this error with your suggestion.
When I use mdrun -rerun to calculate the local pressure, another error occurs:
Fatal error:
Rerun trajectory frame step 600000 time 600.000000 has too small box dimensions
What does this mean?
It means your box is too small. What are the box dimensions in that frame, and
what are the cutoffs you are using?
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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