[gmx-users] minimum distance between the protein and its mirror image

[Justin Lemkul]

On 8/29/16 9:20 PM, OuyangYanhua wrote:
> The minimum protein-image distance is less than the value 2.0nm, such as t around 1.6nm above. Does it mean my simulation is failed in the box size set?

Please read the first sentence of my previous reply.

-Justin

>> 在 2016年8月29日，下午8:58，Justin Lemkul <jalemkul at vt.edu> 写道：
>>
>>
>>
>> On 8/29/16 5:02 AM, YanhuaOuyang wrote:
>>> Hi,
>>>   I am running a REMD of a disordered protein, I visualized the trajectory in VMD and I found that the protein is very close to the box edge.
>>>   Then I use "gmx mindist " to  check  if a protein has seen its periodic image during simulation. When I used the command "gmx mindist -f remd_01.pdb -s remd.tpr -od mindist.xvg -pi" I choose the 1 group---protein. I choose some data from  mindist.xvg, they are as follow:
>>>        0        2.800  5.225  7.200  7.200  7.200
>>>        2        2.793  5.136  7.200  7.200  7.200
>>>        4        2.804  5.002  7.200  7.200  7.200
>>>        6        2.777  5.176  7.200  7.200  7.200
>>>        8        2.820  5.187  7.200  7.200  7.200
>>>        10       2.871  5.043  7.200  7.200  7.200
>>>        12       2.788  5.089  7.200  7.200  7.200
>>>        14       2.882  4.892  7.200  7.200  7.200
>>>       ................
>>>        5154     4.153  3.415  7.200  7.200  7.200
>>>        5156     4.222  3.483  7.200  7.200  7.200
>>>        5158     4.154  3.608  7.200  7.200  7.200
>>>        5172     3.607  4.124  7.200  7.200  7.200
>>>        5174     3.556  4.140  7.200  7.200  7.200
>>>        5176     3.303  4.430  7.200  7.200  7.200
>>>        5178     3.291  4.297  7.200  7.200  7.200
>>>        ...................
>>>        5880     1.659  5.595  7.200  7.200  7.200
>>>        5882     1.787  5.564  7.200  7.200  7.200
>>>        5884     1.718  5.575  7.200  7.200  7.200
>>>        5886     1.669  5.654  7.200  7.200  7.200
>>>        5888     1.636  5.752  7.200  7.200  7.200
>>>        5890     1.590  5.761  7.200  7.200  7.200
>>>        5892     1.620  5.786  7.200  7.200  7.200
>>>        5894     1.513  5.791  7.200  7.200  7.200
>>>        5896     1.523  5.908  7.200  7.200  7.200
>>> I set the short-range VDW and electrostatic cutoffs=1.0 nm, the distance between the outside of protein and the edge of box is 1.0 nm. the Minimum distance to periodic image ranges from 1.5 nm to 4.2 nm from the data above. While the deal value should be at least 2.0 nm, which is double the cutoff.
>>> Do anyone knows the simulation is normal and if a protein has seen its periodic image during simulation?
>>
>> It has not seen its periodic image with cutoffs = 1.0 nm.  You have a very thin shell of water around the protein, though, which means there could be some artificial ordering, but whether or not that's enough to seriously perturb the dynamics is not immediately clear.
>>
>>> which group should I choose when i using gmx mindist, protein, C-alpha or some else?
>>>
>>
>> Protein.  You need to verify that all protein atoms behaved correctly.  CA atoms are unlikely to ever see their own periodic images unless you have done something horribly wrong in setting up your box.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu <mailto:jalemkul at outerbanks.umaryland.edu> | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul <http://mackerell.umaryland.edu/~jalemkul>
>>
>> ==================================================
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List <http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List> before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists <http://www.gromacs.org/Support/Mailing_Lists>
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users <https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users> or send a mail to gmx-users-request at gromacs.org <mailto:gmx-users-request at gromacs.org>.
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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