[gmx-users] Umbrella sampling

[Justin Lemkul]

On 12/3/17 8:01 AM, rose rahmani wrote:
> 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
>> I don't know why this doesn't work since yesterday?!!!!...anyway...
>>
> I used trjconv for just one frame for example conf2000;
> trjconv -f conf2000.gro -n index.ndx -s pull.tpr -o new_conf2000.gro -pbc
> whole
>
> so protein turned into to its normal shape, but i'm not sure does it makes
> sense or not?! is that right? if it's right, another problem is;
>   protein is getting out of box, should i use trjconv for centering?
>
> Thank you for your attentions

A "whole" molecule only matters for visualization. It has no impact on 
physical interactions computed by mdrun.

-Justin

-- 
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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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