Questions tagged [molecular-dynamics]

The tag has no usage guidance.

Filter by
Sorted by
Tagged with
0
votes
0answers
15 views

Generating intercalation site in DNA for custom sequence

Thank you for your help. Can anybody please tell me how I can generate an intercalation site in DNA at the base pairs I am interested on. I appreciate if you can please guide me to any tutorials or ...
0
votes
0answers
24 views

Drug-DNA complex simulation using AMBER

I want to carry out the simulation of drug-dna complex by placing the drug molecule at particular site in my DNA sequence (intercalating site). I have PDB files of both drug and DNA sequence. I will ...
1
vote
1answer
55 views

GROMACS RMSF Result Analysis Problem

This is RMSF for protein from GROMACS after 100ns simulation- I have few questions- Residue numbers are starting from 1650 to 1850, has it ignore LIG and HOH as residues? There are three lines, so ...
1
vote
0answers
23 views

Sending chimera MD to remote computer

I am using Terminal to try to run Chimera MD simulations on a remote server/computer. I have been able to successfully connect using the command ssh username@detroit05 (and then entering the password)....
1
vote
2answers
189 views

How to make a video of a gromacs gmx dump standard output with VMD

I did gmx trjconv on GROMACS trr file to generate a .xtc file, and then used ...
0
votes
0answers
42 views

Ligplot: how to define path in Ubuntu

I installed Ligplot on Ubuntu and have a question. When I open a docking I get the error: Unable to create log file in temporary directory: C:/tmp . I already tried to change the path in several ways ...
0
votes
0answers
143 views

Tutorial for DESMOND steered molecular dynamic simulation

I would like to perform a DESMOND steered molecular dynamic simulation. Til now, I found that I can use the biasing force plugin. Is there any tutorial about how to do this type of simulation?
3
votes
1answer
143 views

Gromacs molecular dynamic simulation throwing error during minimization

I am trying to investigate a membrane proteins influence on a lipid bilayer using molecular dynamics. I am new to MD and trying to run my first simulation. I have built the simulation input files ...