How to install ORCA in gromacs 4.6.5 ?

More Kesavan Ekambaram's questions See All

How to compute the evolution of local interactions in the particular regions of the protein ?

Dear All, I would like to study the evolution of local interactions in the particular regions of the protein over the dynamic trajectory. Could you please help me out with the suitable...

10 November 2018 2,481 3 View

How to find the dihedral angle of particular residue over the period of simulation time?

Dear Friends, I would like to perform the dihedral angle calculation of particular residue over the period of simulation time. Could you please help me out in creating the ndx file using make_ndx...

02 March 2018 6,387 3 View

How to perform the PIEDA calculation for the receptor-ligand residues using FMO ?

Dear All, Im trying to compute the PIEDA for the receptor-ligand residues using the FMO calculation. Could you help me in providing the steps to create the input put file for running the...

10 November 2017 3,680 2 View

How to calculate the host-guest binding affinity using quantum mechanics

I'm trying to find out the binding affinity between the host-guest complex using Mopac. I have only the complexed and uncomplexed files. It would be helpful if someone could explain me with the...

05 June 2017 2,300 4 View

How can I find which dssp version works with gromacs 5.0.2 version ?

I have installed gromacs 5.0.2 version and tried to perform secondary structure analysis ,but there was a fatal error showing use -ver option . i tried using the -ver 2 in the command line still...

02 March 2015 4,137 23 View

GC-MS retention index prediticon?

Hello experts, Does anyone know any free software about retention index prediction ?

08 August 2024 7,403 2 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

Can anyone provide me with molecular docking softwares/ websites?

Molecular docking software/ websites?

02 August 2024 8,704 7 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

I am working on my Master's thesis on the biogeography of the genus Ruagea and I would like to ask, could someone help me to check whether my result?

I created a file with my outgroup and ingroup species using Beauti, ran it in BEAST, viewed it in Tracer, and then used TreeAnnotator to create a file that I imported into RASP. Could someone...

28 July 2024 2,979 1 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

Which software tools are best for enhancing diagnostic accuracy in chest X-ray imaging using image reconstruction and neural networks?

I am reaching out to seek your valuable advice and recommendations regarding the best software tools to use for this research. Specifically, I am looking for software with a user-friendly...

22 July 2024 3,794 1 View

How to test multivariate outlier in STATA?

Hey all, I need help testing for multivariate outliers using STATA for my master thesis. The literature recommends the Minimum Covariance Determinant (MCD) (Verardi & Dehon, 2010). I found the...

22 July 2024 8,821 2 View