[gmx-users] dimer split

[Clarke, Benjamin (NIH/NIDDK) [F]]

Yao,

I have had similar problems with my dimer being Œsplit' by the pbc.
Running this series of trjconv commands on your trajectory may help.

gmx trjconv -s md.tpr -f md.xtc -o md_nojump.xtc -pbc nojump
option 0
gmx trjconv -s md.tpr -f md_nojump.xtc -o md_cluster.xtc -pbc cluster
option 1
option 0
gmx trjconv -s md.tpr -f md_cluster.xtc -o md_mol.xtc -pbc mol
option 0
gmx trjconv -s md.tpr -f md_mol.xtc -o md_PBC.xtc -pbc cluster
option 1
option 0

Best,
Ben



On 11/5/15, 11:14 AM, "Justin Lemkul" <jalemkul at vt.edu> wrote:

>
>
>On 11/5/15 10:56 AM, xy21hb wrote:
>> Dear all,
>>
>> I have a two-identical dimer protein, and I am interested in the
>>chain-chain interaction.
>> However, after long MD, the two chains are separated far from each
>>other though I used PBC.
>> In fact, the chains should be quite close.
>>
>
>You should spend a bit of time reading about what "using PBC" means; your
>dimer 
>isn't actually split.
>
>> I guess GROMACS treats the chains as A and B, and restrain each
>>individually.
>
>You should not restrain chains to fit some preconceived visualization
>convenience.
>
>> I wonder if there is any way GROMACS  can consider it as a whole, or
>>maybe other solutions.
>>
>
>This is what trjconv is for.  Re-image the trajectory, centering on one
>of the 
>chains or some interfacial residues in one monomer.
>
>-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 | (410) 706-7441
>http://mackerell.umaryland.edu/~jalemkul
>
>==================================================
>