Questions tagged [molecular-dynamics]

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1answer
103 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 ...
1
vote
2answers
83 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 ...
1
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0answers
21 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)....
0
votes
1answer
20 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 ...
0
votes
0answers
37 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
107 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?