[gmx-users] multiple replica trajectory analysis

[vijayakumar gosu]

Dear Gromacs users,



I have simulated a phosphorylated protein with 3 replicas (for 300ns). I
concatenated the three replicas (total 900ns) for the analysis
(1_2_3_trj_50ps.xtc). When I perform analysis the protein does not include
the 3 phospho residues. However when I analyzed each replica independently,
protein considers all the residues including phospho residues. I am
confused whether I am doing anything wrong when concatenating the
trajectories. I performed analysis using 1_trj.tprfile from the first
replica. Please someone suggest which .tprfile has to be used for analysis
from 3 replicas. I have given a command below.


echo 4 4 | gmx rms -f 1_2_3_trj_50ps.xtc -s 1_trj.tpr -o 1_rmsd.xvg -tu ns

Select group for output

Group     0 (         System) has 43190 elements

Group     1 (        Protein) has  2927 elements

Group     2 (      Protein-H) has  2302 elements

Group     3 (        C-alpha) has   292 elements

Group     4 (       Backbone) has   876 elements

Group     5 (      MainChain) has  1169 elements

Group     6 (   MainChain+Cb) has  1443 elements

Group     7 (    MainChain+H) has  1454 elements

Group     8 (      SideChain) has  1473 elements

Group     9 (    SideChain-H) has  1133 elements

Group    10 (    Prot-Masses) has  2927 elements

Group    11 (    non-Protein) has 40263 elements

Group    12 (          Other) has    38 elements

Group    13 (            T1P) has    26 elements

Group    14 (            S1P) has    12 elements

Group    15 (             NA) has    16 elements

Group    16 (          Water) has 40209 elements

Group    17 (            SOL) has 40209 elements

Group    18 (      non-Water) has  2981 elements

Group    19 (            Ion) has    16 elements

Group    20 (            T1P) has    26 elements

Group    21 (            S1P) has    12 elements

Group    22 (             NA) has    16 elements

Group    23 ( Water_and_ions) has 40225 elements


If i check for independent replica, using the below command

echo 4 4 | gmx rms –f 1_trj_50ps.xtc -s 1_trj.tpr -o 1_rmsd.xvg -tu ns

Select group for output

Group     0 (         System) has 43190 elements

Group     1 (        Protein) has  2965 elements

Group     2 (      Protein-H) has  2334 elements

Group     3 (        C-alpha) has   295 elements

Group     4 (       Backbone) has   885 elements

Group     5 (      MainChain) has  1181 elements

Group     6 (   MainChain+Cb) has  1458 elements

Group     7 (    MainChain+H) has  1469 elements

Group     8 (      SideChain) has  1496 elements

Group     9 (    SideChain-H) has  1153 elements

Group    10 (    Prot-Masses) has  2965 elements

Group    11 (    non-Protein) has 40225 elements

Group    12 (          Other) has 40225 elements

Group    13 (            SOL) has 40209 elements

Group    14 (             NA) has    16 elements

is it ok to make index file (protein+phosphoresidues) for analysis of the
concatenated trajectory.

Please advise me

Thanks a lot
Gosu