[gmx-users] About densmap tool

;? Thanks in advance Yasser -- Yasser Almeida Hernández PhD student Institute of Biochemistry and Molecular Biology Department of Chemistry University of Hamburg Martin-Luther-King-Platz 6 20146 Hamburg Germany +49 40 42838 2845 yasser.almeida.hernan...@chemie.uni-hamburg.de office: Grindelallee 117

[gmx-users] CG lipid diffusion coefficient

nding on the molecule in question)." (J Phys Chem B. 2009 Feb 5; 113(5): 1501–1510.) The value I get is 2 orders of magnitude higher of a comparable value of 6 um^2/s. Would this make sense? Regards Yasser -- Yasser Almeida Hernández PhD student Institute of Biochemistry and Molecular Biology

[gmx-users] Help with gmx select

as within 0.6 of (group PO4_DOPG_upper or group PO4_DOPG_lower)' But it returns the list of all atoms numbers of every interacting residue. I want ONLY the residue number. Any idea? Thanks in advance Yasser -- Yasser Almeida Hernández PhD student Institute of Biochemistry and Molecular Biology

[gmx-users] contacts

? At the end what I want is to get per-residue contacts between the protein and the PO4 beads, to map them on the protein to see which region have more contacts. Thanks in advance. Yasser -- Yasser Almeida Hernández PhD student Institute of Biochemistry and Molecular Biology Department

Re: [gmx-users] Temperature in CG production runs

lipids at different temperatures using different FFs, showing little differences. In my case I have a bilayer with DPPE, DOPE, POPE, DPPG, DOPG, POPG and CDL, plus a membrane protein, so I think regular physiological 310K is the best, right? Best Yasser -- Yasser Almeida Hernández PhD student

[gmx-users] Temperature in CG production runs

difference in physiological terms. What temperature would you recommend in my case? Thanks in advance and best regards Yasser -- Yasser Almeida Hernández PhD student Institute of Biochemistry and Molecular Biology Department of Chemistry University of Hamburg Martin-Luther-King-Platz 6 20146

[gmx-users] Coordinates transformation

comparable 2D maps? Thanks in advance. Regards Yasser -- Yasser Almeida Hernández PhD student Institute of Biochemistry and Molecular Biology Department of Chemistry University of Hamburg Martin-Luther-King-Platz 6 20146 Hamburg Germany +49 40 42838 2845 yasser.almeida.hernan...@chemie.uni

[gmx-users] Membrane simulation analysis - membrane thickness and area per lipid

is the previous approach from the APL calculated in FATSLiM, APL@Voro, GridMAT-MD? 3 - Which is the best method for the membrane thickness calculation. Thanks Best Yasser -- Yasser Almeida Hernández PhD student Institute of Biochemistry and Molecular Biology Department of Chemistry University

[gmx-users] 2D density maps

web site, reported in https://www.sciencedirect.com/science/article/pii/S0009308413000236?via%3Dihub. Thanks in advance Yasser -- Yasser Almeida Hernández PhD student Institute of Biochemistry and Molecular Biology Department of Chemistry University of Hamburg Martin-Luther-King-Platz 6 20146

[gmx-users] Water tracking along simulation

. Thanks in advance. Yasser -- Yasser Almeida Hernández PhD student Institute of Biochemistry and Molecular Biology Department of Chemistry University of Hamburg Martin-Luther-King-Platz 6 20146 Hamburg Germany +49 40 42838 2845 yasser.almeida.hernan...@chemie.uni-hamburg.de office: Grindelallee

[gmx-users] 2D maps

guidelines in this regard? Thanks in advance Best regards Yasser -- Yasser Almeida Hernández PhD student Institute of Biochemistry and Molecular Biology Department of Chemistry University of Hamburg Martin-Luther-King-Platz 6 20146 Hamburg Germany +49 40 42838 2845 yasser.almeida.hernan

[gmx-users] Running GROMACS on cluster

by a membrane protein, detergent, water and ions. Thanks in advance Yasser -- Yasser Almeida Hernández PhD student Institute of Biochemistry and Molecular Biology Department of Chemistry University of Hamburg Martin-Luther-King-Platz 6 20146 Hamburg Germany +49 40 42838 2845 yasser.almeida.hernan

[gmx-users] Segmentation fault error during run

that is the reason. The system seems to be well equilibrated. Any thoughts? Thanks in advance. Best Yasser -- Yasser Almeida Hernández PhD student Institute of Biochemistry and Molecular Biology Department of Chemistry University of Hamburg Martin-Luther-King-Platz 6 20146 Hamburg Germany +49

[gmx-users] Running GROMACS in cluster with SGE

the Ubuntu repository in each node. Could this be the reason for the poor performance? Should I compile GROMACS from source code on the cluster (cluster optimized)? Thanks in advance Yasser -- Yasser Almeida Hernández PhD student Institute of Biochemistry and Molecular Biology Department

Re: [gmx-users] Adding detergent to simulation box - SOLVED

I solved the problem adding NG, water and ions in that order. Cheers Yasser On 10.01.2017 13:25, Yasser Almeida Hernández wrote: Hello all, I am trying to build a system containing a membrane protein, water, ions and NG detergent (beta-nonylglucoside). A conflict arise when I try to add

[gmx-users] Adding detergent to simulation box

command), none NG molecule is added. On the other hand if I build the solvated box with the protein and NG, and then add the ions, the NG molecules are destroyed/disordered and clustered in the box edges. Any thoughts? Thanks in advance Yasser -- Yasser Almeida Hernández PhD student Institute

Re: [gmx-users] Box dimensions variation

stiffish wire like structure aligned along z). Cheers, Tsjerk -- Yasser Almeida Hernández PhD student Institute of Biochemistry and Molecular Biology Department of Chemistry University of Hamburg Martin-Luther-King-Platz 6 20146 Hamburg Germany +49 40 42838 2845 yasser.almeida.hernan

[gmx-users] Box dimensions variation

in advance -- Yasser Almeida Hernández PhD student Institute of Biochemistry and Molecular Biology Department of Chemistry University of Hamburg Martin-Luther-King-Platz 6 20146 Hamburg Germany +49 40 42838 2845 yasser.almeida.hernan...@chemie.uni-hamburg.de office: Grindelallee 117, room 250c

Re: [gmx-users] Laptop features for MD simulations - recommendations

Hi Dries, Let's say that the price is irrelevant right now. Just imagine an hardware with all the ideal features for the calculations. Thanks all for your answers. Best Yasser -- Hi Yasser, Could you give us an idea of the price range you're looking at? I'd probably try to

[gmx-users] Laptop features for MD simulations - recommendations

Hi all, I want to buy a laptop suitable and powerful enough for MD simulations with GROMACS (mostly membrane/protein systems). Could you recommend optimal features for this goal? Thanks Yasser -- Yasser Almeida Hernández PhD student Institute of Biochemistry and Molecular Biology

Re: [gmx-users] Laptop features for MD simulations - recommendations

Dear Joao, I am aware that laptops are not the proper hardware to run MD simulations. I do my runs in workstations designed for that purpose. The hardware I want to buy is not just for simulations, but for general private/work purpose, but I would like to have a device robust enough to run

[gmx-users] PBC in membrane protein system

coordinates, also results in splitted coordinates. I've tried several trjconv option with any success. How can I get the protein centered in the membrane? Thanks in advance Yasser -- Yasser Almeida Hernández PhD student Institute of Biochemistry and Molecular Biology Department of Chemistry University

[gmx-users] mdp files

= 3e-4 3e-4 ref-p= 1.0 1.0 Thanks in advance Yasser -- Yasser Almeida Hernández PhD student Institute of Biochemistry and Molecular Biology Department of Chemistry University of Hamburg Martin-Luther-King-Platz 6 20146 Hamburg Germany +49 40 42838 2845 yasser.almeida.hernan...@chemie.uni

[gmx-users] Custom elastic network of a membrane protein

an elastic network, lets say the TM helices, excluding other parts of the protein, ej. soluble domains, with martinize.py (or any other tool)? Thanks Yasser -- Yasser Almeida Hernández PhD student Institute of Biochemistry and Molecular Biology Department of Chemistry University of Hamburg

Re: [gmx-users] Membrane protein insertion

Particles with Coulombic Interactions (http://pubs.acs.org/doi/abs/10.1021/ct501047e) - is this the formula intended? Best regards, Andreas -- Yasser Almeida Hernández PhD student Institute of Biochemistry and Molecular Biology Department of Chemistry University of Hamburg Martin-Luther-King-Platz

[gmx-users] Membrane protein insertion

, but normally it is better to fix the problem Any thoughts? Thanks in advance -- Yasser Almeida Hernández PhD student Institute of Biochemistry and Molecular Biology Department of Chemistry University of Hamburg Martin-Luther-King-Platz 6 20146 Hamburg Germany +49 40 42838 2845

Re: [gmx-users] Membrane protein insertion/orientation methods

. -- -- Yasser Almeida Hernández PhD student Institute of Biochemistry and Molecular Biology Department of Chemistry University of Hamburg Martin-Luther-King-Platz 6 20146 Hamburg Germany +49 40 42838 2845 yasser.almeida.hernan...@chemie.uni-hamburg.de office: Grindelallee 117, room

[gmx-users] Membrane protein insertion/orientation methods

Hi all, Among the methods available, which one is the best/more rigorous/popular for membrane protein insertion/orientation in model bilayers (InflateGRO, Memembed, g_membed, etc.)? Thanks in advance Yasser -- Yasser Almeida Hernández PhD student Institute of Biochemistry and Molecular

[gmx-users] Gromacs 5.0.5 compilation error

] Error 2 I installed the last version of CUDA toolkit libraries. Thank in advance for your help. Yasser -- Yasser Almeida Hernández PhD student Department of Chemistry Institute of Biochemistry and Molecular Biology University of Hamburg Martin-Luther-King-Platz 6 20146 Hamburg Germany +49 40