Fatemeh Razavi

9 Questions 3 Answers 0 Followers

Questions related from Fatemeh Razavi

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...

07 July 2016 293 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...

06 June 2016 6,924 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...

01 January 2016 8,802 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...

12 December 2015 2,038 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?

09 September 2015 2,954 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?

08 August 2015 1,510 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...

07 July 2015 1,620 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...

01 January 1970 2,651 0 View

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

Dear users I ran simulations with 128 DPPC/DMPC .I have the output of 10 ns simulation. If I want to draw a plot of area per lipid vs time then how can I proceed? Any gromacs tool comes out which...

01 January 1970 2,123 2 View