MD Simulation in GROMACS 5.0 at a specific pH?

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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

01 February 2017 10,054 0 View

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 9,046 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 ?

06 July 2016 3,473 8 View

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...

06 July 2016 3,120 0 View

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

I need normal Pancreatic cell lines

08 September 2015 1,483 0 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)

02 March 2015 5,806 5 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.

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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.

02 March 2015 7,631 19 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

Are there instances where molecules with larger molecular weights exhibit greater mobility than those with smaller molecular weights?

Hi, I know that low molecular weight (MW) molecules generally tend to have higher mobility, while high molecular weight molecules tend to have lower mobility. However, in my experimental...

06 August 2024 1,495 2 View

For an in-vitro drug release study, what molecular weight cut-off (MWCO) dialysis bag is required for a 117 kDa protein?

kindly reply me. Thanking you in advance.

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How to start a Molecular Dynamics Simulation?

Is it possible to conduct a molecular dynamics simulation to see the effects of a specific carbohydrate on the structure of lipids (e.g., micelle structure)? I am a beginner in this field and plan...

03 August 2024 3,371 3 View

Which will be the best software for the Hydration shell analysis with molecular dynamics?

I am using a windows system, what software I should use for hydration shell analysis with molecular dynamics?

02 August 2024 3,143 4 View

Can anyone provide me with molecular docking softwares/ websites?

Molecular docking software/ websites?

02 August 2024 8,704 7 View

When I simulate for S parameters using ADS, I have faced this issue that I have attached. Please anyone clarify me?

...

31 July 2024 1,671 3 View

Can we patent a process flow diagram developed using a process simulator but no actual cases is carried out?

Can we patent a process flow diagram developed using a process simulator but no actual cases is carried out? For example consider a process for certain product manufacture where a new process flow...

31 July 2024 781 1 View

CAD File of human's & rat's respiratory airways ?

Dear all, I am working on particle deposition in human's & rat's respiratory airways using CFD and I am looking for the 3D CAD file for my simulations (STEP or IGES format). If somone has such...

29 July 2024 1,092 2 View

How to restart MD without using checkpint file in GROMACS?

Dear All Gromacs User I would like to restart MD without using checkpint .cpt files? I heard there is a way for acheiveing this. Any input and sugegstions are most welcome. Thanking You Budheswar

29 July 2024 3,084 8 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