Does anyone know how it is possible to plot area per lipid headgroup versus simulation time?

More Fatemeh Razavi's questions See All

Does any one have experience working with matpack/Xmatrix?

I plot thickness.dat files with xmatrix and gnuplot but I cannot plot area per lipid.dat files neither with Xmatrix nor with Gnuplot. Does anyone know the corresponding command line for Gnuplot...

06 July 2016 299 2 View

Does any one know how I can observe my area per lipid GridMAT-MD ouputs (.dat file format) using gnuplot or Xmatrix?

I simulated DPPC60%-DMPC40% +1AFO model membrane with Gromacs 4.5.4 and now I'm in analyzing step. I wanted to calculate area per lipid headgroup and bilayer thickness of the membrane so I used...

05 June 2016 6,930 0 View

Does any one know how it is possible to make movie in pymol installed on windows 7 ultimate?

I want to make movie from my molecular dynamics simulation outputs. Pymol was suggested to me, when i read its tutorial, i noticad that it is more usefull for mac systems. can any one guide me...

31 December 2015 8,816 1 View

Can any one help me with an error in GridMAT-MD?

I'm trying to use GridMAT to get the area per lipid and thickness so I installed activeperl on my laptop (on windows) and put the three necessary files in and ran this command:> perl...

11 December 2015 2,052 2 View

In the simulation of KALP15 in DPPC, Can we use mdout.mdp files for our energy minimization step, after making necessary changes?

In the simulation of KALP15 in DPPC, when we run grompp command, one of the outputs is mdout.mdp. can we use these files for our energy minimization step, after making necessary changes?

08 September 2015 2,972 0 View

Why did KALP-15_processed.gro file in Justine KALP in DPPC not include hydrogens of alpha carbon for GLY residue number 1?

i want to know that this loss of atoms does not cause errors in simulation results?

07 August 2015 1,525 1 View

Can anybody tell me if it is necessary to remove all water crystals in pdb file for protein molecular dynamics simulation by gromacs ?

I used to remove all water crystals from pdb file before starting simulation same az what I learned from "lysozyme in water" justine tutorial, but I met some one in a seminar, who told me we must...

06 July 2015 1,635 6 View

Does anyone know what is the difference between using and not using .cpt file from previos simulation run in order to extend simulation time?

I simulated DPPC60%-DMPC40%+protein bilayer system for 100 ns. Now I want to run another simulation for 50 ns on this system. I wonder if its nessecery to use .cpt file from the previous md run. I...

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Gromacs first step of minimization ?

I have face this problem anyone help me how to solve this issue ?which is below Fatal error: There are inconsistent shifts over periodic boundaries in a molecule type consisting of 78 atoms. The...

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How to start a Molecular Dynamics Simulation?

Is it possible to conduct a molecular dynamics simulation to see the effects of a specific carbohydrate on the structure of lipids (e.g., micelle structure)? I am a beginner in this field and plan...

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Which will be the best software for the Hydration shell analysis with molecular dynamics?

I am using a windows system, what software I should use for hydration shell analysis with molecular dynamics?

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Can we patent a process flow diagram developed using a process simulator but no actual cases is carried out?

Can we patent a process flow diagram developed using a process simulator but no actual cases is carried out? For example consider a process for certain product manufacture where a new process flow...

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Inquiry on Maximum Nucleic Acid Volume for 2.5 mL Liposome Solution?

I am currently working on a project involving liposomes and need to determine the maximum volume of siRNA that can be added to a 2.5 mL liposome solution with a total lipid concentration of 10...

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How to restart MD without using checkpint file in GROMACS?

Dear All Gromacs User I would like to restart MD without using checkpint .cpt files? I heard there is a way for acheiveing this. Any input and sugegstions are most welcome. Thanking You Budheswar

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How to prepare a molecule for molecular dynamics calculations?

If I want to calculate molecular dynamics (Gromacs), do I first need to optimize the geometry of the molecule? For example, I first draw the molecule in Avogadro, and then what? I guess I can't...

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How to Import Blade geometry from CAD file in ANSYS design modeler?

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Optimal siRNA Volume for Complexation with Liposomes in a 2.5 mL Solution with 10 mg/mL Lipid Concentration?

How much volume of siRNA can I add to 2.5 mL of liposomes with a total lipid concentration of 10 mg/mL?

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How to dispose off lipids waste?

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Sarath Chandra Dantu

You can either use GRID-MAT http://www.bevanlab.biochem.vt.edu/GridMAT-MD/ or g_lomepro (http://www3.mpibpc.mpg.de/groups/de_groot/g_lomepro.html)

And then you can use your favorite plotting tool like xmgrace or gnuplot to plot the outcome

Hossein Rezaei

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