[gmx-users] Umbrella sampling

[rose rahmani]

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


>
> -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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