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MOSAICS-NIH / MOSAICS

A collection of tools for characterizing membrane structure and dynamics within simulated trajectories of molecular systems.
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Mean squared displacement (MSD) #6

Open BadelBF opened 2 days ago

BadelBF commented 2 days ago

Hi Nathan, I'm trying to measure the mean squared displacement (MSD) but the Lipids aren't recognized by lipid_msd_mpi. I tried using the cards as described in the manual by the Figure 4-6.

There are  0 lipid types in the selected leaflet (both) as summarized below: 
 index       type       count 

You have selected (-crd) the following lipid types: 
 index       type       count 

     0       POPE           0 
     1       POPG           0 
     2       PVCL           0

I found the same Issue when applying z_coord_mpi, but was solved adding the biomolecules by the tag -lf_prm. I'm tried the same way, but there is no -lf_prm for lipid_msd_mpi :

 $ lipid_msd_mpi -h 

Description: Lipid MSD is an analysis tool designed to compute the mean square displacement for lipids in the xy plane as a 
function of time. This should yield a straight line where the slope is proportional to the diffusion coeficient. 

        To use this program please enter the following command line options. 

        -traj   R    S    Input trajectory file (xtc, trr, pdb, gro)
        -ref    R    S    Refference file (pdb, gro)
        -o      O    S    Output trajectory file (xtc, trr, pdb, gro)
        -stride O    I    Read every 'stride' frame
        -b      O    I    Skip frames before this number
        -e      O    I    Skip frames after this number
        -lsq    O    S    Index for lsq fitting (ndx)
        -lsq_d  O    I    Dimension for lsq fitting (3:x,y,z 2:x,y)
        -lsq_r  O    I    Reference structure for lsq fitting (0:ref 1:first_frame)
        -crd    R    S    Selection card (crd)
        -msd    R    S    Output data file with MSD data (dat)
        -dt     R    F    Time between analyzed frames (accounting for stride, ps)
        -h      O    -    print help options__

Finally, I tried to add the head and tail of the lipid on leaflet_finder.h file, but not worked. I reaaly appreciate your help. All the best.

bernhardtna commented 2 days ago

Hi BadelBF. Thank you for reaching out for help. From reading your description, I believe you were on the right track when attempting to add the lipid types to the leaflet finder with the -lf_param tag. This option was intended to be available for the Lipid MSD program like it is with Z-coord, and I have now added this option to Lipid MSD. You should thus be able to complete your analysis if you install the latest version. Hope this helps.