[gmx-users] Umbrella sampling
jalemkul at vt.edu
Tue Nov 28 16:02:24 CET 2017
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.
> On Tue, Nov 28, 2017 at 5:11 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>> On 11/28/17 12:23 AM, rose rahmani wrote:
>>> 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.
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
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>> jalemkul at vt.edu | (540) 231-3129
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Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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