[gmx-users] multiple replica trajectory analysis

[Justin Lemkul]

On 5/2/19 3:19 AM, vijayakumar gosu wrote:
> 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.

You can do that, or add the phosphorylated residues to residuetypes.dat. 
The fact that it doesn't show up in one case is mysterious, but either 
you are working on a different computer with a properly updated 
residuetypes.dat (in $GMXLIB or in the working directory) or you are 
using a different GROMACS version that similarly does not recognize S1P 
and T1P as protein residues.

-Justin

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

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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