How to improve the performance by using NAMD for MD on windows OS?

More Dr. Rohan Meshram's questions See All

What is the exact difference between restart files and restart.old files generated as output during NAMD simulations?

When one Performs MD simulations using NAMD. It generates restart files coordinates (.coor), velocity (.vel) and xsc (.xsc) files. It also generates restart files with extension .old. My question...

08 September 2019 7,230 3 View

Any idea regarding alpha and beta values in LIE molecular dynamics simulation of MHC-Epitope complex?

Hi, We are trying to perform MD simulation of MHC-Epitope complex and infer free energy following Linear Interaction Energy method. I know that the van der Waals and Electrostatic terms of bound...

09 October 2015 5,448 0 View

How can I keep my protein inside a water-box throughout simulation using NAMD?

I am trying to run a production run of 1 nano second in NAMD. Everything is OK till first few hundred Picoseconds. But after that my protein runs out of water-box. please have a look at frames of...

11 December 2014 1,920 5 View

Regarding amino acid nomenclature, are there are software or codes that revert alternative names of Histidine (HSE/HID) to normal HIS?

I have a molecular dynamics trajectory and I wish to perform further study on the last frame. While generating PSF and during course of MD simulation, NAMD and VMD changes 3 letter code of...

10 November 2014 4,131 5 View

Any idea about good online tutorial for doing Steered molecular Dynamics simulation using Constant Force Pulling method using NAMD?

Dear all I have DNA-ligand as well as protein-ligand system and I wish to do Steered molecular Dynamics simulation using Constant Force Pulling method using NAMD. I just need to know if you guys...

08 September 2014 2,666 2 View

Need help in relating time scale of MD simulation with 'numstep' and 'timestep' values using NAMD

I wish to know the simple relationship between 'numstep' and simulation time. I mean, if I wish to run a one nanosecond simulation what should be the value that I should put in front of the...

05 June 2014 5,848 4 View

Can anyone help with python scripts to analyze AutoDock results?

I am using PyRx interface for running AutoDock 4.2 After docking I get .dlg files as usual. now i wish to create complexes of poses obtained from dlg file. There are these two python scripts to...

04 May 2014 5,532 2 View

Problem running 64 bit verson of NAMD on Windows7

I have downloaded NAMD 2.9 for Win64-MPI. I downloaded the .zip file, extracted it and tried to run the program. But it gave the following error message "msmpi.dll file is missing". I am sure that...

11 December 2013 3,008 10 View

Are there instances where molecules with larger molecular weights exhibit greater mobility than those with smaller molecular weights?

Hi, I know that low molecular weight (MW) molecules generally tend to have higher mobility, while high molecular weight molecules tend to have lower mobility. However, in my experimental...

06 August 2024 1,495 2 View

For an in-vitro drug release study, what molecular weight cut-off (MWCO) dialysis bag is required for a 117 kDa protein?

kindly reply me. Thanking you in advance.

05 August 2024 7,727 4 View

How to Add Missing Water Molecules in Protein-Membrane Simulations?

I have protein-membrane simulations (PDB, PSF, DCD) and have noticed that water molecules near the protein are not visible in the simulations. How can I fix this issue? Is there a way to place the...

04 August 2024 1,200 2 View

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...

03 August 2024 3,371 3 View

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?

02 August 2024 3,143 4 View

Can anyone provide me with molecular docking softwares/ websites?

Molecular docking software/ websites?

02 August 2024 8,704 7 View

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...

31 July 2024 781 1 View

CAD File of human's & rat's respiratory airways ?

Dear all, I am working on particle deposition in human's & rat's respiratory airways using CFD and I am looking for the 3D CAD file for my simulations (STEP or IGES format). If somone has such...

29 July 2024 1,092 2 View

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

29 July 2024 3,084 8 View

AutoGrid and Autodock 4.2.6 window opens for 1 second then closes and there is no output files?

Good day, I am a student trying to work on Autodock for a project regarding Ligand-DNA interaction so i am quite new to molecular docking. i have followed tutorials and did all the steps...

28 July 2024 2,136 4 View

Ivan Anashkin

Molecular dynamics does not require a lot of memory. Adding more memory will not affect on performance. Instead this better to use GPU for simulation.

Alexey Nikitin

@Ivan Anashkin

On the contrary, if algorithm uses the lists of atoms pairs it require a lot of memory. This can greatly limit the size of the model.