Re: [gmx-users] How to solve the "LINCS WARNING" problem (???)

> > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > Today's Topics: > >1. Re: How to solve the "LINCS WARNING" problem (???) >2. RIN (Residue interaction net

[gmx-users] atomselection for index group of cyclic rings

Dear all, I am interested in measuring the distance between two cyclic rings present in the residues and ligands over time. Can you kindly suggest how to go about this? Specially, if i am interested in measuring the distance between the center of the two rings over time. Thank you -- Regards,

[gmx-users] RIN (Residue interaction network) for protein ligand interactions

Dear All, I am interested in viewing the Residue Interaction network during a protein - ligand simulation. Can someone suggest an easy way to go about it? I tried to use gRINN tool but I guess it doesn't work if ligands are present. Thanks in advance. -- Regards, Prasanth. -- Gromacs Users

Re: [gmx-users] no subject

Hello Faisal, Easiest way to do this is by navigating to the MD files tab and download the "Gromacs 4.5.x-5.x.x 54a7" below this warning - "*Warning!* This molecule contains non-standard atom types not included in the standard GROMOS 54A7 forcefield..." The folder contains the procedure to

[gmx-users] Can you help regarding this

Dear Kushal, Regarding the first error, I feel that you have done a few mistakes while updating your topology section as your system has more atoms than what is in the topology. Kindly go through the tutorials on this site - http://www.mdtutorials.com/gmx/index.html, to get a picture on how to do

[gmx-users] charting Ligand's movement in the binding pocket

Dear All, I am interested in charting the trajectory of the ligand with respect to the residues of the binding pocket, during the simulation. May be representing the center of mass of the ligand as a dot at each frame, would help us see the path traced by the ligand in the pocket, during the

[gmx-users] Issues with energy minimization of a membrane protein

Dear all, I am interested in carrying out a simulation of mPGES-1 protein (PDB id: 4yl3), which is a homotrimer. I am using POPC membrane; equilibrated for 100 ns for this purpose. I was able to align and insert the protein into the membrane using lambada align and inflategro programs,

Re: [gmx-users] convergence of bilayer simulation

Dear Justin, Thank you for your inputs. After using GridmatMD. I obtained the following results - Area per lipid is 62.696275 ± 0.545 Angstrom (square) Average thickness of the upper and lower membranes is 3.66 ± 0.28 Angstrom (square) I am also attaching the graphs for lateral displacement of

Re: [gmx-users] convergence of bilayer simulation

Dear Roshan, Thank you for your response. I thought that the lipid also behaves as a solvent in the case of membrane simulation. we even try to make sure the set temperature (starting from equilibration) is beyond the phase transition temperature. I wonder what sort of impact this will have on

[gmx-users] convergence of bilayer simulation

Dear all, I am carrying out a simulation to equilibrate lipid bilayer (POPC) in water, which I would like to use for membrane protein simulation. Is there a way to know, if a lipid bilayer simulation has converged or not? -- Regards, Prasanth. -- Gromacs Users mailing list * Please search the

Re: [gmx-users] Membrane protein simulation isotropic vs semiisotropic

oogle.com/a/sssihl.edu.in/file/d/14yDNhlBJKbhhgFdpIYtr7SGhQIMoJrq6/view?usp=drive_web> On Fri, Jun 14, 2019 at 12:09 PM Prasanth G, Research Scholar < prasanthgha...@sssihl.edu.in> wrote: > Dear all, > > Can someone please tell me if it is okay to use isotropic pcoupltype for a &g

[gmx-users] Membrane protein simulation isotropic vs semiisotropic

Dear all, Can someone please tell me if it is okay to use isotropic pcoupltype for a membrane protein simulation? Are there any disadvantages? Also, why is semiisotropic preferred over isotropic, in membrane protein simulations.. Thank you. -- Regards, Prasanth. -- Gromacs Users mailing list

Re: [gmx-users] compressed pbc box at the end of simulation - membrane protein with ligand

Dear Bratin, Thank you for your prompt response. would using an isotropic pcoupletype have any effect on a membrane protein simulation? If we provide same ref_p values for all three axis (as in the above case)in a semiisotropic treatment, would this have the same effect as isotropic treatment? I

[gmx-users] compressed pbc box at the end of simulation - membrane protein with ligand

Dear all, I am carrying out a simulation of membrane protein with a ligand. I am using DPPC [slipids (http://www.fos.su.se/~sasha/SLipids/Downloads.html)]. I had modified amber 03 ff by including the non-bonded and bonded parameters from slipids website as suggested in the tutorial by Justin (

[gmx-users] How to extract frames from a simulation at regular intervals and make a new trajectory?

I am interested in extracting 300 snapshots from a 30ns simulation with an interval of 100 ps and create a new trajectory for analysis (MMPBSA). files md_0_30.xtc, md_0_30.tpr.. new trajectory to be named as md_analysis.xtc. Request you to help me in this regard. Thank you. -- Regards,

[gmx-users] PCA analysis and comparing extreme1 pdbs of two different simulations

Dear all, I am interested in carrying out PCA analysis on two trajectories- 1) protein in water and 2) protein with ligand in water. I would like to know, if there is a procedure by which we can compare the extreme1 pdbs (constituted by the movements that contribute to EV1) from both the

Re: [gmx-users] concatenate tpr files for PCA analysis

Dear Subhomoi and Mark, I was able to overcome the problem by using the new tpr file, as suggested. Thanks for the help. Regards. -- 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

[gmx-users] concatenate tpr files for PCA analysis

Dear all, I am interested in carrying out pca analysis of protein with ligand (complex). I had carried out a simulation for 20 ns and extended it by 10 ns (making it a 30ns simulation). I had extracted protein trajectories from both the simulations and joined them together using -cat flag. I

[gmx-users] clarity w.r.t pca analysis of protein and ligand complex

Dear all, I am interested in carrying out PCA analysis of protein and ligand complex in order to understand which ligand binds to protein and restricts the relative movement of the chains of receptor during simulation. I have carried out four simulations of 30 ns each - 1) with just the protein

Re: [gmx-users] Help with respect to processing protein with FE2+

Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com On Mon, Dec 24, 2018 at 8:41 PM Prasanth G, Research Scholar < prasanthgha...@sssihl.edu.in> wrote: > Dear all, > > One of the proteins of my interest, has a FE2+ in the center and as it

Re: [gmx-users] Help w.r.t enhancing the node performance for simulation

;-std=c++11;-O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast; CUDA driver:8.0 CUDA runtime: 8.0 Thank you in advance. On Sat, Dec 29, 2018 at 2:33 PM Prasanth G, Research Scholar < prasanthgha...@sssihl.edu.in> wrote: > Dear all, > I was able to overco

[gmx-users] Problem w.r.t simulation with a Heme containing protein

Dear all, I have tried to process the heme containing protein using GROMOS 54a7. Although I am able to convert the pro.pdb to pro.gro, I am getting a warning sign, like this, -- While running pdb2gmx -f pro.pdb -o pro.gro . . . Before cleaning: 9225 pairs

[gmx-users] Procedure for processing docked complex from Autodock vina

Dear all, I am trying to run a simulation of protein docked with ligands of interest. I have used autodock vina for the docking. Do i need to convert the receptor.pdbqt to receptor.pdb before proceeding? Do i need to add missing hydrogens in this step? Also the protein of interest has four

Re: [gmx-users] Help w.r.t enhancing the node performance for simulation

Dear all, I was able to overcome the issue, by introducing the command "mpirun -np x" before the command. Here is the exact command- mpirun -np 32 gmx_mpi mdrun -v -deffnm md_0_10 -cpi md_0_10.cpt -append -ntomp 4 Thank you. On Fri, Dec 28, 2018 at 12:12 PM Prasanth G, Resear

[gmx-users] Help w.r.t enhancing the node performance for simulation

Dear all, Though the GROMACS was configured with MPI support during installation. installation cmake.txt I am able to use only one MPI process on the node for the simulation. This happens

[gmx-users] Help with respect to processing protein with FE2+

Dear all, One of the proteins of my interest, has a FE2+ in the center and as it plays a main role in the activity of the protein, it cannot be removed. Can you please suggest a solution. I have tried with CHARMM and GROMOS, with no success. After reading a bit, I understood that, the charges on

Re: [gmx-users] Protein-ligand complex simulation and ATBserver file

340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == On Wed, Dec 19, 2018 at 3:05 PM Prasanth G, Research Scholar < prasanthgha...@sssihl.edu.in> wrote: > Dear Sir, > > I am runnin

Re: [gmx-users] Protein-ligand complex simulation and ATBserver file

Dear Sir, I am running GROMACS 5.1.4 on a server. I had converted the protein(pdb2gro) using the latest GROMOS forcefield. As per your suggestion, I had downloaded the parameter files from ATB server. As per the readme file from the server (in the parameters folder), i had updated my topol.top