[gmx-users] Fwd: thread_GROMACs_question

[Dallas Warren]

First off, you should keep this on the emailing list.  I have included the
emailing list in the reply.  No need to take it to private email.

Did you read the link that I sent with the reply?  You even have the
simulation box visualised with the vmd screen shot you sent, so that should
be a big clue to you what is going on.  Have a play with the vmd periodic
images tab, it should very quickly make sense.

>From what gmx distance says, I don't think you need to use any pbc
processing before doing the calculations, it takes pbc into consideration.
The processing you did has probably messed things up, most likely the
nojump.  And the graphs indicate this fact too.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Wed, 24 Oct 2018 at 09:32, Antonio Carlesso <antonio.carlesso at gu.se>
wrote:

> Dear Warren,
>
> I am a PhD student at the University of Göteborg (Sweden).
>
>
> Since you should be an MD expert I would like to ask you one more stuff
> regarding this thread (hope I will not bother you):
>
>
> https://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/msg34909.html
>
>
>
>
>
>
>
>
>
> Do you have any reason why  calculating the distance over time between
> two pair of atoms (Oxigen of the ligand VS nitrogen of the Lysine in the
> protein) using gmx distance in GROMACs (Figure 1) and VMD(figure 2)  does
> not match ?
>
>
> *Figure1.* Values obtained with gmx distance in GROMACS
>
>
>
>
> *Figure 2.* Value obtained for just one of the previous graph (green one)
> using VMD.
>
>
>
>
>
> for my believe the ligand is actually moving away (picture below).
>
>
>
>
>
> Thank you for your possible help!
>
>
>
> Best regards,
>
> Antonio
>
>
>
>
>
> p.s. to deal with PBC I first make my system “whole” , extract the first
> frame from the trajectory to use as  reference, and then use trjconv -pbc
> nojump with that first frame as reference
>
> aprun -n 1 gmx_mpi trjconv -s md_0_500.tpr -f md_0_500.xtc -o
> md_0_500_whole_dt50.xtc -pbc whole -dt 50
>
>
>
> aprun -n 1 gmx_mpi trjconv -f md_0_500_whole_dt50.xtc  -s md_0_500.tpr -b
> 0 -e 1  -o 1st_frame.gro -pbc mol –center
>
>
>
> aprun -n 1 gmx_mpi trjconv -s 1st_frame.gro -f md_0_500_whole_dt50.xtc -o
> md_0_500_whole_dt50_nojump.xtc -pbc nojump
>
>
>
>