I performed MD for apoprotein after this I want to calculate potential
energy or short-range and long-range energy and enthalpy "per residue"
please help me how can I do this?
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_Lis
I performed MD for apoprotein after this I want to calculate potential
energy or short-range and long-range energy and enthalpy "per residue"
please help me how can I do this?
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_Lis
I performed MD for apoprotein after this I want to calculate potential
energy or short-range and long-range energy and enthalpy "per residue"
please help me how can I do this?
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_Lis
Dear researcher
As we know, we add only specific ions including Na and Cl to simulation box
for conducting molecular dynamics simulation. The question is raised is why
we don't add other ions to simulation box that are existed in the cell
environment, for example, phosphate or potassium?
It is reas
Dear researcher
I want to measure the following parameters for a part of a protein
Intramolecular potential energy
protein surface potential
Ebond, bond length potential energy contribution
Eangle, bond angle potential energy contribution
Etorsion, torsion angle potential energy contribution
Dear researcher
I want to check the effect of an SNP (Single-nucleotide polymorphism) in my
protein structure. To do this, I once simulated a protein in the Wild Type
state and once again mutated for 100 nanoseconds.
After performing the MD, The defect of many articles I have read in
literatures,
Please explain why this article has been accepted
Please refer to the RMSD chart
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0064364
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
*
In many cellular signaling pathways in cancer cells, the expression of many
genes rises. One result of this excessive expression is cellular traffic
and unwanted interactions between proteins. Therefore, it is important to
examine the interactions and identify the amino acids involved in the
intera
In many cellular signaling pathways in cancer cells, the expression of many
genes rises. One result of this excessive expression is cellular traffic
and unwanted interactions between proteins. Therefore, it is important to
examine the interactions and identify the amino acids involved in the
intera
Hi
I gonna MD simulation a protein that contained a zinc ion for build
topology I used from the amber99sb force field Atomic charge is written
"+2" in topology.
I wanted to ask if this charge is correct or should be calculated in a
different way?
"PDB id 4row"
sincerely
--
Gromacs Users mailing l
I'm going to examine the interaction between the two proteins using
molecular dynamics simulation by gromacs, so I downloaded pdb code 5op1
from the rcsb , which has two protein(Complex). I want to create a gap
between two protein, and then with the same coordinate Put these two
proteins in a box a
hello
I'm using Gromacs with
charm27.ff force-field.I adding a new residue (NAG) in force field
I have a problem with water molecules in my system: During
minimization, I have this message:
step X: Water molecule starting at atom XXX can not be settled.
Check for bad contacts and/or reduce the
12 matches
Mail list logo