Error problem running NAMD simulation software?

More Ashutosh Kharwar's questions See All

Please suggest some good quality and free journal with very short response time for MEMS, piezoelectric energy harvester research?

27 August 2020 994 4 View

Can anyone help in understanding the type of analysis required for publishing in ABDC Journal?

I have completed a research paper in which I have tested and validated through factor analysis antecedents to consumer involvement for organic food products. I tried to publish in a few good...

10 August 2020 1,077 3 View

Is there any online recommendation tool to suggest the most relevant journal for a given topic?

Usually, the publishing houses like Elsevier and Springer have their own recommendation system to suggest the best journal to submit the paper for a given topic and abstract. But is there any 3rd...

10 April 2020 4,796 6 View

What are the suitable clustering models for high dimensional data?

I have a dataset with 290 rows and 35000 features. What are the consequences of running clustering techniques (such as Hierarchical) on the whole dataset and what should be the most suitable...

24 February 2020 8,620 7 View

In VASP GUI (MEDEA) how to visulaize charge density when it is already calculated?

Iam not able to see the plot for charge density though i did the calculation part. CHGCAR files are also creaed but uamnot able to analyse. please help

16 February 2020 8,743 3 View

How to create the simulation environment for the restricted vibration of cantilever with the help of the stopper?

A cantilever is fixed at on end and free to vibrate at another end. When there is no stopper at the free end, the vibration of the cantilever results in the maximum swing. But, when we place a...

06 February 2020 9,622 1 View

What are the drawbacks of Calinski-Harbasz score in clustering?

I am running a hierarchical clustering exercise and trying to evaluate it with different measures like Calinski-Harbasz score and Silhuette score. Could anyone tell or point to any document...

20 December 2019 4,103 3 View

Kindly let me know if algal oil extractor is available that can be used at large scale without using solvent ?

Dear Scientist I am very curious to know the oil milling machine in practice to extract oil from dried microalgae powder and if possible please share all details... If we don't want to use...

06 December 2019 4,369 1 View

How to test repeated measures - 2 way Anova?

I have measurements from several experiments on a specific combination of two different factors, say A and B. From each experiment, I calculate three types of values (to check the performance of...

18 November 2019 2,587 4 View

Are you interested in publishing your book chapters in the field of Nanotechnology and Medicinal Plants in a book by Taylor & Francis?

Are you interested in publishing your book chapters in the field of Nanotechnology and Medicinal Plants in a book by Taylor & Francis publisher?

21 October 2019 6,043 57 View

How to analyze a particular region of my simulation box in GROMACS?

Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...

03 March 2021 9,989 2 View

Why almost every element would be metallized in sufficiently high pressure and low temperature?

(This statement is from wikipedia, BTW). What is so special about metallic bond that is limiting high-P low-T state of a matter (as long as individual atoms exist, not white dwarf of neutron star...

02 March 2021 3,309 2 View

How to formulate Energy minimization in Molecular dynamics simulation for alloys using meam potential?

during MD simulation, the atoms are not moving as per required. The problem (as per my observation) lies in energy minimization technique. upon application of tensile strain in x or y direction,...

22 February 2021 380 5 View

Magnetismic Gravity in the universe?

MAGNETISMIC GRAVITY What is magnetism? Something magnetic has a + and - charge. If 2 + or - are pushed if + and - are pulled. But what is the main reason for this? Why does magnetism have a pull...

21 February 2021 9,538 3 View

Has anyone succeeded in capturing uranium atoms in a fullerene structure?

Additional questions are: What are the encapsulating atoms? How difficult was the process and what rates were achieved? What factors most seriously affect the economics?

20 February 2021 3,134 5 View

How to get the vector of a specific vibration mode in phonon dispersion?

For example, I have this phonon dispersion(Fig. 1), and now I would like get vector of atoms which describes TA1 in P. I know v_sim can show vibrational animation of specific mode, but I do not...

20 February 2021 4,332 4 View

What are the potential shell well and atomic solvation parameters for the boron atom?

I have a protein-ligand docking project. The ligand contains boron atoms that are not detected by Autodock software. To solve this problem, it is necessary to introduce the boron atom to...

19 February 2021 1,236 1 View

How to combine two geometries in LAMMPS ?

I am trying to simulate contact angle of water on a quartz slab using LAMMPS. I have created and equilibriated the quartz slab and the water cluster separately. Now I want to create a composite...

17 February 2021 5,884 2 View

Rdf of atoms from a COM or point in lammps or VMD?

Hello all, as I understand there isn't any straight way to get an rdf of atoms from the center of mass or a coordinate of specific atoms in lammps. I wonder if anyone know any trick or way to get...

16 February 2021 2,517 2 View

What is error #2070 in gaussian.how we do resolve it?

We want to ONIOM calculation in gaussian16. However, gaussian doesn't work. What should we do? Atom 15 layer R linked to atom 85 is also bonded to atom 161 in layer M bad...

15 February 2021 7,766 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.