[gmx-users] Umbrella sampling

[Justin Lemkul]

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.
Assistant Professor
Virginia Tech Department of Biochemistry

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