How to do simulation using DMSO as solvent?

21 November 2023 0 10K Report

I am trying to solvate my solute in DMSO but each time when I try to solvate using the gmx solavte command it adds only 7 DMSO molecules to the box rather than completely filling the box. Can any one tell what I am doing wrong?

Badges
Science topic

More Arzoo Jangra's questions See All

What is the physical meaning for the following equivalent circuit?

Can anyone help me to find out the Rs = Solution resistantce and Rct= Charge transfer resisistance of the following equivalent circuit. specifically, which R should I take as Rct. I got this...

12 May 2024 4,358 2 View

Error while calculating MEP using orca 5.0 ?

Hello folks, I recently started using orca 5.0 version to calculate Molecular electrostatic potential but after the first step it generated .densities file instead of .scfp file (which was...

13 February 2024 7,400 4 View

Which tool to use to get single unit cell from an entire lattice?

Hello everyone I generated the lattice of ice using genice2 software and now i want a single unit cell from that lattice and i am unable to get that. For this purpose i tried using vesta software...

23 January 2024 7,461 0 View

Installation problem with genice2 software?

Hello folks, I am trying to install genice2 software.Even after satisfying the per-reqistics and installing completely when i try to run it the error i am getting is " cell: np.ndarray[3, 3] =...

26 December 2023 376 3 View

From where I could learn MOST/Software for tsunami inundation?

I am a PhD student looking to gain expertise in tsunami inundation modeling using the MOST Software. Can you please suggest reliable sources or educational materials where I can learn in-depth...

01 November 2023 9,474 0 View

From where I could learn MOST/Software for tsunami inundation?

I want to learn MOST/Commit Software for tsunami inundation. Is there any source? Kindly help me in this regard if anybody knows. Thanks in advance

22 August 2023 3,482 0 View

I am trying to install the software genlocdip used to calculate dipole moment and I am getting error in compilation ?

The error is Cannot read module file ‘yaml_output.mod’ opened at (1), because it was created by a different version of GNU Fortran compilation terminated.

03 July 2023 9,604 1 View

What does O refers to the name Toluidine blue O dye?

I have searched on Google and got two or three answers for the same. O for oxazine or due to the ortho position of methyl group. Please clarify.

10 May 2023 8,681 2 View

Issue with HEK293 revival?

i am really new in cell culture laboratory. Last week, i have tried to revive HEK293 cell line cryo (stored in -80 degree )from april 2021. these pictures are from 5th day of revival. i am...

13 April 2023 7,219 3 View

Is there any modeling software that can be used to assess evacuation scenarios in the event of a tsunami?

Disaster and Evacuation Management

29 March 2023 3,807 3 View

Which solvent is better to dissolve with secondary metabolites extracted from fungi?

I work on MCF7 cell cell for anticaner purpose and I wa to do drug preperation the drug ( secondary metabolites extracted from Aspergillus) My question which solvent is better with these secodary...

03 August 2024 4,725 2 View

I need to dissolve stigmasterol for an animal experiment, it hasn't dissolved in either DMSO or vegetable oil. Can anyone recommend the best solvent?

Hello everyone, I need to dissolve stigmasterol for an animal experiment, but it hasn't dissolved in either DMSO or vegetable oil. Can anyone recommend the best solvent for stigmasterol?

01 August 2024 7,504 2 View

What is the suitable solvent of MIL-100 for chemotherapy?

I synthesised a nanocarrier by conjugation MOF (MIL-100) with folic acid for use in chemotherapy but the samples didn't dissolve completely in aqueous solution or DMSO. Instead, they only...

19 July 2024 8,522 0 View

Kraft lignin and MMA(Methyl meth acrylate) free radical polymerization for synthesis of thermoplastics?

I am conducting free radical polymerization using Kraft lignin and MMA, with DMSO serving as the solvent and there is also an initiator. Following the reaction, I obtain a solution, but I am...

15 July 2024 9,827 1 View

Regarding solubility of Dorsomorphin in DMSO ?

I'm using Dorsomorphin (C24H25N5O) as one component in dual SMAD inhibition of pluripotent stem cells to differentiate into neurons alongwith SB431542. Now as to solubilizing 10mg SB in DMSO for...

11 July 2024 4,832 0 View

Does anyone have suggestions for this esterification?

I have a very polar alcohol (soluble in MeOH, H2O, partially in heated DMSO). And a long chain fatty acid that I would like to couple. I can't find a common solvent for them. I can form the...

24 June 2024 9,319 0 View

Why is iPSC in bad condition?

I saw the iPSC about a week after holding the stock (12 well and 3 stocks) and there were very few cells attached, and some cells were differentiated. I wonder what the problem is. The plate is...

12 June 2024 6,087 0 View

I am carrying out MTT Assay using HeLa cells but the absorbance values are really less, can anyone please help?

I have seeded HeLa cells in a calculation of 10000 cells per well in a 96 well plate. Then I went for treatment in the next day. Then at last, I added 7ul of 5mg/ml solution of MTT reagent into...

12 June 2024 1,460 3 View

Is it possible to do FACS on snap frozen cells ?

Is it possible to do FACS on snap frozen cells ? They were isolated and directly dropped in liquid N2. They were not frozen with DMSO or FBS.

11 June 2024 8,915 0 View

Which statistical test for mRNA stability changes upon treatments ?

Hello, I discovered that a compound that I use, which get integrated into RNA, might have an unspecific impact on mRNA stability of a gene of interest. To confirm that, I pretreated my cells for...

10 June 2024 276 2 View