On 11/28/17 10:00 AM, rose rahmani wrote:
Would "pull_geometry=periodic-distance" be another solution for it?
No. That affects how the reaction coordinate distance is calculated, not
the PBC treatment, which is intrinsic to any simulation using PBC.
-Justin
On Tue, Nov 28, 2017 at 5:11 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 11/28/17 12:23 AM, rose rahmani wrote:
Hello;
I took 2000 configuration from trajconv. Amino acid is in its normal shape
till almost conf1000.gro(and a little more). But in for example
conf1300.gro amino acid was disintegrated. What does it mean? Would you
please help me?
Bonds can't break and molecules can't "disintegrate" - what you're seeing
is probably a result of PBC.
http://www.gromacs.org/Documentation/Terminology/Periodic_
Boundary_Conditions
-Justin
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Justin A. Lemkul, Ph.D.
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303 Engel Hall
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Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
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