Does any one have experience working with matpack/Xmatrix?

06 July 2016 263 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 6,862 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 8,781 1 View

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

11 December 2015 2,000 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 2,920 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?

07 August 2015 1,490 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 ?

06 July 2015 1,599 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 2,630 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

How to analyze a particular region of my simulation box in GROMACS?

Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...

03 March 2021 9,989 2 View

Arena simulation - how do i model the following model in ARENA (see description) (new to ARENA)?

Hello, I'm fairly new to ARENA and I have the following problem: I have two queues in which, in each queue, a different order type arrives (both having an arrival rate of exponential 10). Order...

02 March 2021 2,431 3 View

Is there any test to determine the cardiovascular risk of patients with obesity? from the perspective of obesity?

We found tests to determine cardiovascular risk taking into account lipid profile, blood pressure, age, history of diabetes, other laboratories. But when weight is involved, there is a paradox. I...

02 March 2021 6,036 1 View

Why are the velocities so high in my Boussinesq approximation Fluent simulation?

Hello, I have a mechanism where air rises due to convective flows. In this simulation, nothing is driving the air except this. I understand that the Boussinesq approximation only works for small...

02 March 2021 4,910 3 View

How to repeat an operation on an atom selection for multiple times in PyMol?

Hi, I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol...

02 March 2021 4,569 4 View

How to calculate average trend in maximum annual NDVI from MODIS?

I am wanting to calculate the average trend in maximum annual NDVI in Iceland from 2010-2020 using MODIS MYD13Q1 V6. How would I do this? I have currently inserted the NDVI bands from the MODIS...

02 March 2021 752 2 View