[gmx-users] gromacs.org_gmx-users Digest, Vol 128, Issue 97

[jinxin]

Hi Tsjerk    thank you very much ! as you said, the protein get splite and i can't get it back wiht command 'trjconv -pbc nojump -center'. however, i can use the command 'trjconv -fit rot+trans' to get the protein back. i don't know what the reason is. is my system broken?thank you very much!
>
>Hi Jinxin,
>
>The distance should be at least half of the cut-off distance, such that the
>total distance (twice the distance between protein and 'box edge') will be
>larger than the cut-off distance. So you should be fine. Now, if the system
>undergoes large conformational changes, that may still cause direct
>interactions. However, the most common cause to find violations of the
>minimum distance is that the molecule gets split over PBC. Make sure that
>your protein is whole before running g_mindist.
>
>Cheers,
>
>Tsjerk
>
>On Mon, Dec 22, 2014 at 11:19 AM, jinxin <18819028611 at 163.com> wrote:
>>
>> Dear everyone,
>>        During my simulation,  i set the option '-d 1.2' creates a buffer
>> of 1.2 nm between the outside of the protein and the edge of the box.  In
>> the mdp file, i set the rcoulomb=rvdw=1.4, cutoff-scheme = Verlet. After
>> the simulation, i use g_mindist -pi to analyzed the minimal distance
>> between periodic images , i found some values are less < 1.4. i think the
>> promlem is that i should increase the value of '-d 1.2'. someone tell me
>> that the value should twice the cut-off distance from the
>> next nearest image of itself. however, i found some publication set the
>> '-d 1.2', the coulomb and van der Waals cutoffs of 1.4 nm. please tell me ,
>> if i set the set the rcoulomb=rvdw=1.4, which value of '-d ' should i set ?
>> thank you every much!
>> --
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>
>
>-- 
>Tsjerk A. Wassenaar, Ph.D.
>