[gmx-users] Umbrella sampling

[Justin Lemkul]

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 <jalemkul at 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
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> 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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>>
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==================================================