MD Simulation in GROMACS 5.0 at a specific pH?

More Garima Singh's questions See All

How to do median and quantile normalization of microarray data in GEO which does not have .CEL files?

I want to normalize the GSE data which is in .txt format i.e non-normalized. How to do median and quantile normalization of this .txt file using R? Your help is appreciated Thanks

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How to calculate number of Calcium ions during MD simulation?

I want to add 1mM calcium ions inside my protein simulation box after knowing the number of water molecules in water box. How to calculate the calcium ions? What are the steps in GROMACS to follow...

07 August 2016 8,983 4 View

Is 20ns simulation enough to study 317 amino acid length protein in GROMACS?

My protein is a cysteine protease of 317 aa with a single point mutation. I want to simulate the mutated structure. What should be the time length ?

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Next Generation Sequencing Training?

There is a highly recognized company in the field of Life Sciences/ Bioinformatics- Shodhaka, which is planning to organize high throughput training in Next Generation Sequencing, but they need a...

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Can anyone suggest a pancreatic cell line expressing CASR and SPINK1 gene?

I need normal Pancreatic cell lines

08 September 2015 1,434 0 View

Is there a database of pre-validated Real-Time PCR primers?

I want a database where experimentally validated Q-PCR PRIMERS are available . I am using SYBR Green for real-time PCR. Waiting for your valuable answers.

02 March 2015 4,654 2 View

Is it right to design primers for Real-Time PCR (SYBR-Green) by using coding the sequence as the template?

I downloaded the Coding Sequence s from NCBI and designed primers using Primer-BLAST (NCBI)

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Which is the most validated gene to be used as a control in Q-PCR ?

My Experiment sample is pancreatic tissue. Please help me in deciding the control gene to be analysed by Q-PCR.

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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

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

Thirumal Kumar

@Abel - could you please tell us how to use those ? I have used http://compbio.clemson.edu/pka_webserver. what should i do with this output?

@Lian- could you please tell us how to use those ? I have used http://compbio.clemson.edu/pka_webserver. what should i do with this output?

Dmitri Kireev

Here is a useful thread on this matter. As you will see the problem is protein-specific and does not have a straightforward unique solution.

http://gromacs.org_gmx-users.maillist.sys.kth.narkive.com/djNXyWmM/simulation-at-particular-ph

Garima Singh

@Dmitri, this link is not working. can you send me again