How can I split a Gromacs .tpr file?

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How to do CHARMM to GROMACS conversion?

I have generated a .str file from .pdb file using CGenFF server. But whenever I try to convert the .str file to gromacs specific topology using: python3 cgenff_charmm2gmx_py3_nx2.py JZ4...

24 August 2020 3,593 3 View

During ligand preparation I obtained CHARMM format file from CGenFF and now i want to get gromacs format file. Why following error occurs ?

Command: python cgenff_charmm2gmx.py jz4 jz4_fix.mol2 jz4.str charmm-mar2019.ff Error: Traceback (most recent call last): File "cgenff_charmm2gmx.py", line 47, in import networkx as nx...

20 August 2020 4,869 5 View

I want to write the review papare on seismicity of himalayas, How can I start and specifically bound the arear for research?

PLease guide me so that I can proceed for the structural analysis as well as seisimic analysis , a review type

10 May 2020 5,119 8 View

Is there a possibility to use the water for agricultural purposes in which the algae has grown?

I want to grow algae in *Water* and then want to use that algae for different purposes and also use that leftover water for agricultural purposes. Will there be any harms for the fields by taking...

28 March 2020 757 9 View

What are the best promoters for N-methyl-N-nitrosourea induced mammary tumors in rats?

As N-methyl-N-nitrosourea is a carcinogen used to induced mammary tumor in rats for breast cancer model development and we ran out of carcinogen what could be the possible alternative or the...

19 March 2020 7,587 1 View

For how many days can we store N-Acetyl-D-lactosamine water solution without affecting it's efficacy?

We have N-Acetyl-D-lactosamine 25mg powder from Sigma Aldrich. The required dose is 5mg/Kg or 0.1mg for 20g mouse. The dose is so minute that it is nearly impossible to make fresh doses everyday...

16 February 2020 5,576 1 View

Interpretation of negative interaction but positive direct effects?

How do I interpret the results if all the direct relations between IV, DV and Moderation are positive but moderation effect itself has a negative beta.... Following are my results: IV --> DV...

29 December 2019 922 3 View

How to find the Bader charge of O atom in MO6 Octahedron (M=Ni or TM)?

I ran Bader analysis on VASP and I have ACF.dat file, I can see the charge value of different atoms according to my POSCAR. I also know the charge value for O atom but how can I find bader charge...

11 December 2019 4,942 3 View

What will be chow test interpretation?

Hi, I applied chow test to check whether coefficients are different in two groups(in cross section data). and get following result . what will be interpretation of this result. F( 9, 4597) =...

21 November 2019 7,642 1 View

The coin cell battery which I made is broken, what can be the reason behind that?

I'm making a coin cell battery using NCA as cathode and Li metal as anode. I connected it to check the electrochemical performance but during the first cycle it broke and discharge capacity...

10 October 2019 3,170 5 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

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

Why are the velocities so high in my Boussinesq approximation Fluent simulation?

Hello, I have a mechanism where air rises due to convective flows. In this simulation, nothing is driving the air except this. I understand that the Boussinesq approximation only works for small...

02 March 2021 4,910 3 View

Why the results when using wall thickness and when using shell conduction are different in ansys fluent?

Actually, I am running cfd simulation for a heat exchanger which has two fluids one hot and other one is cold fluid. there is a solid domain between them, which I removed and instead I have used...

01 March 2021 9,537 2 View

Joint behaviour in Abaqus is not captured well?

I am working on roof joint and trying to simulate the behaviour in Abaqus. I am successful in running the model but the final graph does not follow the experimental curve in the negative direction...

01 March 2021 6,661 3 View

In Molecular Dynamics Simulation, how do I make changes to the force field according to my protein?

Hi In Molecular Dynamics Simulation, how do I make changes to the force field according to my protein? I got this error in the add-ion stage: Fatal error "./ amber99sb-ildn-HHH.ff / force...

01 March 2021 8,747 4 View