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?
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
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
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
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
i want to know that this loss of atoms does not cause errors in simulation results?
07 August 2015 1,525 1 View
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
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 2,667 0 View
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 2,141 2 View
How to develop investments in renewable energy sources?
08 August 2024 5,112 3 View
Dear QE-users, In the method where full MS positive mode and PRM mode are used, we always get an incorrect auxiliary gas reading (41 instead of 25). This only happens in this method; other...
06 August 2024 4,953 0 View
Hello guys! Do you have experience running a Oaxaca-Blinder decomposition on R applying person weights. How do you suggest doing it? I have a variable PERWT which gives more information on how...
04 August 2024 6,033 0 View
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...
03 August 2024 3,371 3 View
I am using a windows system, what software I should use for hydration shell analysis with molecular dynamics?
02 August 2024 3,143 4 View
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...
31 July 2024 781 1 View
Hello. Thanks for your consideration to see my question. Recently, I conducted XPS anaylsis of g-CN that is prepared from thermal polycondensation of DCDA, so-called conventional bulk-g-CN,...
30 July 2024 9,824 2 View
Hello Everyone I have a question about structure for connectivity analysis on sources. My goal: preprocess and cut data into trials create headmodels, using template MRI file perform source...
30 July 2024 2,744 1 View
When I run autogrid4 it says: autogrid4: ERROR: Unknown receptor type: "Cr" -- Add parameters for it to the parameter library first! Look forward to your reply.Thank you so much!
29 July 2024 488 0 View
I am trying to run a restart analysis, which imports deformed configurations of parts from a generated ODB file. It runs fine in Windows OS but when I try to run it in Linux OS, it is giving some...
29 July 2024 9,572 3 View