Could I use topology file created by vmd for doing md in gromacs?

19 October 2020 1 8K Report

I am facing a problem to make topology file using cgenff as instructed in Lemkul's Gromacs tutorial. But it didn't work as I couldn't get Networkx of version 1.11 . So, I am trying to find an alternative way. I made my topology file using autopsf builder of vmd. Could I use this topology file for MD simulation in gromacs? I am very new in this field. Please help me. Thanks in advance for any help or suggestions.

Lukas Braun

You can convert between the different file formats with TopoGromacs. Check out this paper: Vermaas, J. V.; Hardy, D. J.; Stone, J. E.; Tajkhorshid, E.; Kohlmeyer, A. TopoGromacs: Automated Topology Conversion From CHARMM to GROMACS Within VMD. J. Chem. Inf. Model.

Badges
Science topic

More Diptendu Roy's questions See All

Which DL architecture is better to work on handwritten data?

I am working in the area of Handwriting recognition for Bangla. As there are many DL architecture, I am confused which one to select.

15 February 2021 4,996 1 View

Do you have any experience of taking astaxanthin supplement?

Astaxanthin is a keto-carotenoids having reddish color. It occurs naturally in certain algae and causes the pink or red color of different seafood especially salmon, shrimp, trout, and lobster....

29 January 2021 7,861 2 View

How to remove/reduce Back Reflection from Objective?

I want to have a optical system where, I focus a beam onto the BFP of a microscope objective. Unfortunately, I always have a strong Back Reflection from the objective. Can anyone suggest me some...

18 January 2021 2,062 8 View

How to calculate binding energy and different interactions from a pdb file of protein-ligand complex?

I have done a docking study by using mcule.inc web-service. I got the .pdb file of my protein-ligand complex from there. As I am using a free student account, I don't have access to more...

14 January 2021 2,321 2 View

Why there is no increase in virus titer after 24 hour of seeding for harvest?

I am working on virus production through bioreactor,my concern is regarding ,no increase in virus titer after 24 hour of seeding for harvest Usually we seed the fermenter and incubate for 72...

05 January 2021 3,860 2 View

How to optimise or tune the hyperparameters of Gaussian Process Regression?

I am working with the algorithm Gaussian Process Regression. I used gaussian process regression module from scikit learn library of python. But I couldn't correlate the hyperparameters of Gaussian...

24 December 2020 4,864 4 View

Can you suggest me how can I use D2O for dissolving chitosan sample for NMR analysis?

I am trying to dissolve chitosan with pure D2O but it is not dissolving. I read some articles that used D2O for dissolving chitosan before 1H and 13C NMR analysis? Do I need to do some...

14 December 2020 6,931 5 View

How many chapters (objectives) are necessary for a standard Ph.D. thesis?

This question is focused on biological, chemical, and material science. I think the answers also will help the future Ph.D. students for writing a good Ph.D. research proposal.

10 December 2020 2,090 34 View

Running a Kruskal-Wallis test on a large sample with a likert scale on excel?

Hi everyone, I would like to run a Kruskal-Wallis test on a large sample with a likert scale. I am having difficulties figuring out how to process with the ''rank_avg'', and rank sum with such a...

05 December 2020 793 3 View

Can someone help me with a code for R software for principal component analysis and even tell me how to arrange the dataset?

I am having a biparental mapping population of rice with dataset of various morphological and post harvest parameters from F6 and F7 and 6 checks in augmented block design.

17 November 2020 6,272 4 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 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

What kind of fluid could I use for a pitfall trap that also does not invalidate molecular testing?

Hi, I want to start testing pitfall trap to obtain ants samples, but I need to conduct molecular analysis on those insects. So, what kind of fluid can I use? Ethanol expires too early and I need...

03 March 2021 5,978 5 View

How to get onecolumn document from standard IEEE ACCESS LateX template?

I have prepared a manuscript in IEEE Latex template, but for some purpose, I need to prepare a word file as well (detailed format is not required). Compared to two column .tex file, one column...

02 March 2021 1,830 3 View

Arena simulation - how do i model the following model in ARENA (see description) (new to ARENA)?

Hello, I'm fairly new to ARENA and I have the following problem: I have two queues in which, in each queue, a different order type arrives (both having an arrival rate of exponential 10). Order...

02 March 2021 2,431 3 View