Error problem running NAMD simulation software?

More Ashutosh Kharwar's questions See All

The Powder XRD pattern of a dinuclear metal complex does not match with the simulated single-crystal XRD pattern. What can be the reasons?

04 April 2024 3,901 4 View

Hi all how one can calculate C:N:P ratio?

Dear all, Will you please let me know how to calculate the carbon, nitrogen, and phosphorus (C: N:P) ratio in wastewater? Is it advisable to measure total COD, nitrogen, and phosphate? or I...

05 February 2024 4,105 3 View

How can i change bond type in pdb file?

Hi i am doing work on a protein which has Cu ion in it but the bond it is making with protein are not matching the reference protein making bond with Cu ion so is there any possible to change the...

23 January 2024 5,999 1 View

Regarding phyco-remediation cattle derived wastewater?

Hello intellect. I am working with an algal consortium to treat wastewater derived from cattle (CRWW). Different dilutions of raw CFWW (FCWW/dH2O; v/v) were used for algal cultivation. As a...

20 January 2024 341 1 View

Does SPHY 2.1.1 or SPHY 2.0.3 model consider Temperature lapse rate?

I have used WFDEI meterological data from the HinduKush Himalaya database provided by FutureWater to force temperature data on my study area. If the model is not considering temperature lapse...

18 January 2024 7,006 0 View

It is possible to implement real time dairy processing plant effluent remediation using algal consortium?

Being a biotechnologist, I am always curious to know the real example where a stakeholder shows enthusiasm and implements an algal consortium or axenic culture to treat raw dairy wastewater...

30 November 2023 6,761 1 View

Re: Running and Installation of SPHY Model?

I'm trying to learn SPHY model but I'm facing some issues in running of SPHY preprocessor model in QGIS 2.8.2 like GDaL open failed and while creating initial maps they get removed automatically....

16 September 2023 7,614 1 View

How to use data of internal resistance vs DoD and entropy change vs DoD for battery modeling in Ansys Fluent?

The battery models available in Ansys Fluent are NTGK, ECM, and P2D. Most of the research articles have done experimental investigations to find the data of internal resistance vs. DoD and entropy...

14 September 2023 7,171 0 View

Virtual Molecular Dynamics showing blank screen after opening .pdb and .gro file ?

it shows this and vmd shows blank screen Info) VMD for LINUXAMD64, version 1.9.4a57 (April 27, 2022) Info) http://www.ks.uiuc.edu/Research/vmd/ Info) Email questions and bug reports to...

30 August 2023 826 0 View

Molecular docking of small substrate have binded strongly but have lower docking energy ?

can we consider -5 kcal/mol binding energy is as good energy for small molecules like serotonin in molecular docking

23 August 2023 7,146 2 View

1. If I can quantize the atom using this hyperbolic spiral and classical physics, could nature do the same?

If we map as a continuous motion an ionising electron (beginning its journey at n=1) in an H atom, a specific hyperbolic spiral appears (see animation). When we solve this spiral formula, we find...

07 August 2024 5,343 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

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 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

Why reactivity isn't increased with more empty spots in valence shell?

If from a geometric perspective the non-halogens, non-noble gases have more empty spots in their valence shell, and the filling/exiting of any of the empty spots in the shell constitutes a...

03 August 2024 4,787 2 View

Why do paired electrons atoms produce no magnetic field lines?

If you think of electrons with spin as bar magnets, you know bar magnets of opposite polarity as long as they're not occupying the same spatial location don't cancel out each other's magnetic...

03 August 2024 3,927 2 View

How can you draw a coordinate bond between a metal and donor atom in metal complexes, using discovery studio visulizer software?

Hello,, The metal complex ligand appears incomplete in the screen of the discovery studio visualizer

30 July 2024 3,354 1 View

How to do pca analysis of c-alpha atom of the protein?

i m interested in pca analysis of c-alpha atoms in gromacs for that i used the following gmx_mpi covar -s mdca.tpr -f mdca.xtc -o eigenvalca.xvg -v eigenvecca.trr -av average.pdb -n index.ndx but...

30 July 2024 1,607 1 View

Why am I observing very high Temperature and Pressure Increase using NPT Ensemble?

Hello everyone, I am running DFT with CP2K software at 1200 K, 1 bar with a periodic system of 64 Al atoms + 2 CO2 atoms. However, I am seeing my temperature slowly increase to >4000 K and my...

22 July 2024 3,177 0 View

How to create parameter and coordinate files for ligand in amber when FATAL error (maybe due to duplicate bond specifications) happens?

Hello, I'm trying to create parameter and coordinate files for a drug (PRG-A01) found on the following page: http://www.probechem.com/products_PRG-A01.html I used the guide made by Michael...

17 July 2024 3,472 3 View

Aashish Bhatt

you can check the following links:

https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2012-2013/3505.html

https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2012-2013/3512.html

Tanushree Das

Presumably, the .psf file didn't have the parameters for OT atom type.

Please check the topology .rtf files as well as the parameter .prm files to look into the atom details.