How are the default parameters derived?

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Water flux inside a pore?

Hi all, I am performing a Molecular Dynamics simulation of a water pore inside a membrane. I am experimenting with some analysis options and I am having a bit of a trouble understanding the water...

01 February 2019 8,941 2 View

Trouble with gmx distance?

Hi, I am trying to calculate the distance between two atoms, which are defined in an index file. The command that I use is: "gmx distance -f output.gro -s prod.tpr -n index.ndx -oav...

07 August 2017 3,395 4 View

Problem running heme proteins on gromacs?

Hi I am trying to simulate a protein containing a heme, using Gromacs and Charm27 force field. When I try to run pdb2gmx I get an error. I have looked the force field directory and found that this...

09 October 2016 3,058 2 View

Temperatures for Replica Exchange Simulations?

Hi, I am trying to simulate a protein using Replica Exchange. By reading at the literature I found what values are needed as a Tmin, Tmax and also the number of replicas. Apart from that there is...

07 August 2016 7,429 1 View

Paper for Replica Exchange MD?

Hi I want to perform an remd simulation of a large protein system. The bibliography I found so far is about small systems and doesn't describe the way they decide on the number of replicas or the...

07 August 2016 3,423 8 View

How to calculate bond force constant for CLA for molecular dynamics ?

I am using Gromacs and I want to edit the ffbonded.itp in oplsaa.ff directory. I have by literature the bond length but I can't find the force constant. Is there a way to calculate it?

05 June 2015 1,926 5 View

Any advice on my problem adding new molecule in aminoacids.rtp - gromacs?

I'm trying to add a molecule in aminoacids.rtp (new user) By looking at the pre defined amino acid entries and the chapter 5 of the manual I started building it up. The fields that the file...

04 May 2015 8,669 4 View

How can I proceed with a molecule.itp in Gromacs?

I have made a molecule.itp file according to the chapter 5 of Gromacs Manual and existing entries in the ff directory I want to use.My problem is that I don't know how to continue, in theory I...

04 May 2015 5,482 3 View

Is it possible to plot the atom-projected band structure using GPAW?

Hi, I'm currently working on a project where I need to plot the atom-projected band structure using GPAW. I've been able to calculate the band structure for my material, but I'm having trouble...

07 August 2024 269 3 View

Gromacs first step of minimization ?

I have face this problem anyone help me how to solve this issue ?which is below Fatal error: There are inconsistent shifts over periodic boundaries in a molecule type consisting of 78 atoms. The...

07 August 2024 2,598 1 View

Should I include H atom into C3N5 when i am doing DFT modelling?

Hi all, my experimental XPS results shown that my C3N5 sample consists of N-H bond, hence in this case I should incorporate the N-H bond into my DFT modelling. However, I do notice several papers...

07 August 2024 8,414 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

How to prepare a molecule for molecular dynamics calculations?

If I want to calculate molecular dynamics (Gromacs), do I first need to optimize the geometry of the molecule? For example, I first draw the molecule in Avogadro, and then what? I guess I can't...

28 July 2024 673 3 View

Why Orca calculations take too loong?

Hello! I am trying to calculate the sumatriptan molecule, but it has been counting for five days and it does not stop. It seems to me that it is too long and I am doing something wrong. Please...

25 July 2024 3,364 5 View

Wrong out put for gmx x2top?

Dear users, I would like to simulate a zeolite structure in gromacs. I got the .cif file from IZA expanded in one direction in Materials Studio and exported a .pdb file. However, when I want to...

24 July 2024 367 4 View

What is the principle/mechanism behind aging of carbon (graphite) containing refractory mix for isostatically pressed refractories?

The resin bonded carbon containing refractories are aged before use. How time of aging is determined? And mechanism behind aging.

23 July 2024 3,205 0 View

MDCI module in Orca software?

Dear Researchers, My question is associated with the "MDCI" method in Orca. Please let me clarify my question using a simple example: Suppose we are going to perform CBS extrapolation using "!...

21 July 2024 1,632 0 View

Why binding energy is in positive number after performing mmpbsa?

I performed mmpbsa of protein-protein complex simulation on gromacs. My binding free energy is +166781. This complex is stable when experimentally produced in wet lab. In index.ndx I grouped...

19 July 2024 4,120 5 View