31 Questions 30 Answers 0 Followers
Questions related from Mohammad Zahidul Hossain Khan
I want to do some magnetic property calculation. For this reason I want to get some idea about this software from some user.
01 January 2019 7,813 0 View
I want to md simulation on nanocluster iron for radiation damage at 300K. Is it difference just for periodic boundary condition or anything else like constant temp, heat sink etc?
12 December 2018 1,712 0 View
I am doing md simulation for radiation damage in FCC iron. Here is my input script: I have tried this script with and without pka velocity and getting exact same simulation. my target is to...
09 September 2018 6,801 0 View
Hi Atomicrex user, I want to generate EAM potential for Fe (FCC structure) also, I want generate for Fe-O. Can anyone help me on that things?
04 April 2018 6,008 0 View
I am trying to follow one journal where potential is complicated to me. I have written my way. Still, it needs several improvements. Can anyone help me with it? Any kind of suggestion would be...
04 April 2018 4,419 2 View
Hi Everyone I want to do MD simulation for radiation damage in FCC iron structure. I have found EAM potential for BCC iron structure. Do you think, I can use same file for my system just...
04 April 2018 7,278 4 View
Dear Lammps users, I am trying to simulate radiation damage on Fe_Fe3O4 structure. I am getiing error which is shown below. ERROR on proc 0: Neighbor list overflow, boost neigh_modify one...
03 March 2018 1,808 2 View
Hi everyone I have attached two image. one is before simulation and another is during simulation. Can anyone tell me why my oxygen particle is not contributing on the simulation? #...
03 March 2018 4,685 2 View
I want to do MD simulation for radiation damage by Si in iron core Iron oxide (Fe-Fe3O4). I want to know, which potential would be good for this system. Do you think EAM force field or ReaxFF...
03 March 2018 2,798 0 View
Hi I want to do MD simulation for Iron_core_iron_oxide. Basically I will see the radiation damage for this iron core oxide shell. I am new in material MD simulation. I have some basic idea for MD...
03 March 2018 1,693 3 View
Hi I am very new for lammps. I want simulate iron core Iron oxide structure. I know there are many things need to run the simulation. but for the beginning i need the geometry structure of iron...
02 February 2018 455 7 View
I want to MD simulate for radiation damage in iron core iron oxide. I am brand new on material simulation. For this reason, I want to first produce the structure. It could be spherical shape or...
02 February 2018 7,777 3 View
Hi I want to do radiation damage in Fe by MD simulation. I have generate the pure iron structure and will use Fe_2.eam.fs for atom pair. I have no idea how to write command for Si+2 which have...
02 February 2018 7,291 5 View
I want to do the md simulation for radiation damage in my material. I have good idea md simulation on protein but radiation damage in material not. So I need help. please help me.
01 January 2018 7,811 5 View
I am looking for MD simulation software for radiation damage measurement in materials. I also need tutorial for that software.
01 January 2018 1,558 2 View
I want to know the software name for embedded atom method using md simulation.
10 October 2017 9,578 6 View
How can i simulate gamma radiation effect on nano particle in molecular dynamics?
10 October 2017 760 4 View
I want to simulate magnetic naonomaterials. Does any one know the software's name for that simulation.
09 September 2017 7,324 0 View
Dear Sir I want to calculate the SASA energy for protein ligand system. I want to use LCPO algorithm base SASA model. I am also gromacs user.
08 August 2017 4,640 1 View
I have protein-ligand system. I have basic idea for energy minimization.mdp parameter. ; integrator = steep emtol = 10.0 emstep = 0.01 nsteps = 500 energygrps = Protein OAI ; nstlist =...
07 July 2017 7,652 2 View
Dear Sir I want calculate the protein's energy from my md_production simulation. Can anyone help me about that?
07 July 2017 4,441 4 View
In gromacs energy file, we use to get the below energy. My question, how can i get vander waals energy and electrostatic energy from them. [Bond], [Angle], [Proper Dih.], [Improper Dih.],...
07 July 2017 7,578 0 View
Does anyone know how to create ligand topology for gaff (general amber force field) force field? I have tried acpype but it is giving me the...
07 July 2017 1,675 1 View
I am calculating average binding energy for protein-protein complex using g_mmpbsa. I have used 0ns to 10ns and 10ns to 20ns and 500frames. I have got different average binding energy for both...
04 April 2017 9,906 1 View
I want to calculate protein-protein binding energy using mmgbsa (molecular mechanics, the generalized Born model and solvent accessibility) for gromacs.
12 December 2016 9,332 3 View
Is it possible to calculate the binding free energy using g_mmpbsa for protein complex? I have followed the tutorial but I could not create the files for two unbound protein and complex (dimer)...
11 November 2016 8,029 2 View
Allocation failure for numerical quadrature. Error termination via Lnk1e in /global/software/gaussian/g09.d01/l703.exe at Thu Oct 16 04:42:02 2014.
10 October 2014 4,616 0 View
In my input file, I want to fix most of the atoms, and want to vary few atoms in cartesian coordinates. How can I do this?
05 May 2014 4,868 4 View
In my pdb file, there are 6 chain identifier. How can i select 2 identifier using vmd or pymol? then i will do md simulation. I want to take B and F identifier and will run for md simulaiton. I...
01 January 1970 1,695 7 View
I am using 1BRS (barnase-barstar) for binding energy calculation using g_mmpbsa. Generally i remove water from the md simulation trajectory and then use trajectory, topology and index file for...
01 January 1970 1,541 2 View
Does any one have any idea, how to solve the below error for NAMD Charm++ fatal error:FATAL ERROR: Low global exclusion count! (17240 vs 17255) System unstable or pairlistdist or cutoff too...
01 January 1970 8,921 3 View
