[gmx-users] Membrane-protein Simulation
Sankaran SV .
119013033 at sastra.ac.in
Mon May 6 12:46:48 CEST 2019
@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-request at 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 <najamuddinmemon63 at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] multiple replica trajectory analysis
> Message-ID:
> <
> CALwxfCL-LCWL5BipdWbEqq1qPqT1-DMP9p3vq4P5n9i5ZcezAQ at 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 <vijayakumargosu at gmail.com>
> 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.
> >
> > Please advise me
> >
> > Thanks a lot
> > Gosu
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> > send a mail to gmx-users-request at gromacs.org.
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 2 May 2019 15:40:49 +0500
> From: Najamuddin Memon <najamuddinmemon63 at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Membrane-protein Simulation
> Message-ID:
> <CALwxfCKA3zE5maW_q9OXckoQPC-AodL7CVSKEHE_+LRPe=
> PLWw at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Yes it is normal to correct .xtc file through -pbc flag
>
> On Thu, May 2, 2019, 12:57 PM Sankaran SV . <119013033 at sastra.ac.in>
> wrote:
>
> > Dear all,
> >
> > We are investigating the hydration dynamics of membrane proteins (AQP
> > embedded in DPPC membrane). The topology and the mdp files for
> simulations
> > was obtained from the MemprotMD database (mdp file:
> > http://memprotmd.bioch.ox.ac.uk/). We modified the temperature of
> > simulation to 310 K since we are interested in the hydration dynamics at
> > body temperature. After 100 ns simulations, we observe that the protein
> has
> > drifted from the center of the bilayer to the periphery. There was no
> > changes in the lipid layers. The apparent movement of the protein
> vanished
> > after pbc correction was performed with centering the protein. Could you
> > please advise if it is common to observe proteins drifting during the
> > simulation and if it is fine to correct it with pbc correction?
> >
> > Thanks.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 2 May 2019 16:29:57 +0530
> From: Saumyak Mukherjee <mukherjee.saumyak50 at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] problem regarding gmx trjconv
> Message-ID:
> <
> CAGCTgrWfyShAAcOJmR3ZMdJJoaSPvWupriJOOgEeeMC+z+A4Cg at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear All,
>
> I have an insulin hexamer, which (because of PBC) apparently breaks into
> pieces after simulation.
>
> To make the molecule whole, I use the following command:
>
> gmx trjconv -f traj.xtc -s md.tpr -o traj_whole.xtc -pbc cluster
>
> or
>
> gmx trjconv -f traj.xtc -s md.tpr -o traj_whole.xtc -pbc mol -ur compact
>
> This command(s) makes each chain (out of the 6) whole, but the chains do
> not come together. So the hexamer as a whole still remains broken.
>
> Is there a way to solve this problem?
>
> Thanks and Regards,
> Saumyak
>
> --
> ===========================
> *Saumyak Mukherjee*
> Senior Research Fellow
> Solid State and Structural Chemistry Unit
> Indian Institute of Science
> Bengaluru - 560012
> ===========================
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 2 May 2019 11:52:25 -0500
> From: Nidhin Thomas <nidhin.thomas0624 at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Electric field applied to a water box
> Message-ID: <0D3209F9-4931-4608-8ACF-7768512857B5 at gmail.com>
> Content-Type: text/plain; charset=us-ascii
>
> Dear all,
>
> I tried to apply a static electric field across a water box. I used
> anisotropic pressure coupling. Details of the pressure coupling is given
> below.
>
> pcoupl = Parrinello-Rahman
> pcoupltype = anisotropic
> tau_p = 5.0
> compressibility = 4.5e-5 4.5e-5 4.5e-5 0 0 0
> ref_p = 1.0 1.0 1.0 0 0 0
> ;
> constraints = h-bonds
> constraint_algorithm = LINCS
> continuation = yes
> ;
> electric-field-y = 0.1 0 0 0
>
> I see that water box size reduced in the direction of application of
> electric field (Y) and increased in X and Z direction.
>
> Original Size = (4 x 4 x 4) nm
> Final Size = (4.3 x 2.8 x 4.9) nm
>
> I would like to know if I made an error in providing the mdp options and
> also the origin of the compression of water box in Y direction.
>
> Thanks a lot for your help!.
>
> Nidhin Thomas
> University of Houston
>
> ------------------------------
>
> Message: 5
> Date: Thu, 2 May 2019 12:54:30 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] gmx trjconv does not produce exact .gro file
> (slightly different box length)
> Message-ID: <505ab4d7-8c25-d35a-c97d-e6a557a767c5 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 5/2/19 5:13 AM, Faezeh Pousaneh wrote:
> > Hi,
> >
> > I notice that gmx trjconv does not produce the exact .gro file (slightly
> > different box lengths).
> > I mean when i run following command
> >
> > gmx trjconv -f NPT.trr -s NPT.tpr -o f.gro -pbc mol -b 2000
> >
> > I get slightly different box length than when I run gmx energy ... and
> > select box-X,Y,Z.
> >
> > Anyone knows why?
>
> .trr and .edr store greater precision. A coordinate file format like
> .gro has limited precision. The same thing happens with coordinates and
> velocities.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
>
>
> ------------------------------
>
> Message: 6
> Date: Thu, 2 May 2019 12:55:41 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] multiple replica trajectory analysis
> Message-ID: <969f1b2e-2144-0b3b-f282-2806f88b02f6 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> 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
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
>
>
> ------------------------------
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
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> send a mail to gmx-users-request at gromacs.org.
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> End of gromacs.org_gmx-users Digest, Vol 181, Issue 7
> *****************************************************
>
--
Sankaran.s.v
bbin
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