Why does npt equilibration generate free space ?

During the nvt it was okay. After the NVT equilibration, short NPT equilibration was performed. During this equilibration, free space generated inside box. Please tell me some possible reasons?

09 October 2018 8,546 0 View

How to convert CHARMM .str to .itp file for GROMACS?

Dear Experts, I generated LIG.str file using CGenFF for a specific molecule. I would like to use GROMACS package. I tried to convert LIG.str file to LIG.itp file. I tried as following command...

31 December 2017 9,258 3 View

How can I know the structure was optimized or not?

Hello, I am very new user of Gaussian. I started the optimization of the connected two amino acids. Calculation was finished, and I would like to get the optimized structure. How can I know...

05 June 2017 7,037 5 View

Which protein structure viewer useful for draw vectors?

01 February 2016 3,326 1 View

Can someone verify my singular value decomposition of 3D helical data?

01 February 2016 8,378 0 View

How do I make a pH dependent simulation of Oligomer structures?

Hello, I want to make pH dependent simulation of dimer, trimer and pentamer structure of peptide. How to make it using AMBER or GROMACS? Can I use H++ server for oligomers? or How to set manually....

31 December 2015 769 2 View

How to fix malloc error during MM-PBSA calculation on AMBER14

Hello, I have got following error during MMPBSA.py calculation for PBSA MD simulation. How to fix it? ******************************************************************** Beginning GB calculations...

10 November 2015 10,029 2 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 does blocking with my immunogenic peptide cause nuclear fluorescence in ICC?

Hi all, I am validating a polyclonal antibody raised against human ANT4, through WB and ICC. In most of my controls, the antibody shows very little off-target binding, but when I pre-incubate the...

03 March 2021 5,999 3 View

How can I calculate the rdf of water molecules around 'Na' ions that are closest(adsorbed) to the nanoparticle(solute)?

Hi, I want to calculate the radial distribution function for water molecules around the Na+ ions adsorbed on the surface of a spherical nanoparticle using the gromacs trajectory dynamically? For...

28 February 2021 5,650 1 View

How can I assign a velocity along one direction to CO2 molecules in a molecular dynamics simulation using GROMACS?

Dear all, I am trying to perform a MD simulation about the interaction between CO2 and a polymer. I create my model, solvate it and perform the NVT and NPT equilibration. Now I am not able to...

26 February 2021 10,014 3 View

How does GROMACS calculate the average structure of proteins?

I want to get a average structure from a pdb file containing multiple models. I used the command below: gmx cluster -f input.pdb -s topol.tpr -cutoff 20 -method gromos -av GROMACS...

25 February 2021 6,314 1 View

How to identify or create correct list from GROMACS options during analysis of trajectory ?

During topology preparation using pdb2gmx Protein_chain_A and Protein_chain_B were identified. However, when production MD was completed and I proceeded to do analysis, I find this list : Group...

23 February 2021 5,065 8 View

No title

23 February 2021 4,014 3 View

How to reduce static electricity of powder after lyophilization?

I am working on synthesizing and then purifying peptides using the SPPS system. After purification of the peptide, the peptide powder is obtained using a freeze dryer. When measuring the powder,...

22 February 2021 10,099 5 View

Can we remove the fmoc group after peptide cleavage?

I have synthesized the peptide using Fmoc based solid phase peptide synthesis. Also I have cleaved the peptide from the resin and lyophilized it, but later realized that, I forgot to deprotect the...

21 February 2021 4,537 3 View

How T cells recognise non-peptide antigens?

This might sound very basic question, but please share with me an explanation of how the T cell is activated when the antigen is not a peptide? What happens? And what are the molecules involved in...

21 February 2021 564 3 View