@email on Membrane protein Simulation:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2019-May/125180.html
Dear Najamuddin Memon
Thanks for your reply. I am a little confused here. Why is the protein
alone drifting? Typically, when we simulate protein only or protein-ligand
systems, the protein along with the co-molecule drifts – and hence we do
pbc correction. But in our case, we observed that the lipid does NOT move.
Only the protein, which is supposedly embedded in the lipid, drifts.
Further, when we proceeded with centering the system with respect to the
protein (which removed the drift), and calculated the number of water
molecules that remained in the interface layer (defined as 4.5 angstrom
from the protein) throughout the simulation, the two numbers were
different. That is, we obtained 16 waters molecules that remained in the
interface layer BEFORE centering and only 5 were found to be in the
interface layer AFTER centering. Would centering affect the number of water
molecules that resides in the hydration layer throughout the simulation?
Would be grateful for any inputs.
Thanks
Sankaran SV
On Thu, May 2, 2019 at 10:27 PM <
gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:
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> Today's Topics:
>
>1. Re: multiple replica trajectory analysis (Najamuddin Memon)
>2. Re: Membrane-protein Simulation (Najamuddin Memon)
>3. problem regarding gmx trjconv (Saumyak Mukherjee)
>4. Electric field applied to a water box (Nidhin Thomas)
>5. Re: gmx trjconv does not produce exact .gro file (slightly
> different box length) (Justin Lemkul)
>6. Re: multiple replica trajectory analysis (Justin Lemkul)
>
>
> --
>
> Message: 1
> Date: Thu, 2 May 2019 15:39:30 +0500
> From: Najamuddin Memon
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] multiple replica trajectory analysis
> Message-ID:
> <
> calwxfcl-lcwl5bipdwbeqq1qpqt1-dmp9p3vq4p5n9i5zce...@mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> When you are trying to join two .xtc files phosphorylated residues will be
> broken. They remain intact when you generate the pdb files or any other
> analysis.xvg from one and single .xtc file that you have suggested before
> running md simulation
>
> On Thu, May 2, 2019, 12:19 PM 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
> >
> > Group10 (Prot-Masses) has 2927 elements
> >
> > Group11 (non-Protein) has 40263 elements
> >
> > Group12 ( Other) has38 elements
