I want to do a simulation with Molecular Dynamics but lack the facilities.
i have open MD web but i only get prepared molecul before running MD simulation,,,how to running MD simulation in this web??without instaling gromacs or amber in my PC?
You have to register first. Then "Start new project" and then you are following the instructions and you can upload a PDB or enter a PDBID and choose a type of process. The interface is not difficult. You can find all you need there.
Hi,
I am a new user of molecular dynamic on web server. At the step of "Gromacs FULL MD Setup", after finished the step, I faced with a problem, when click on download bottom, don't downloaded anything. I couldn't download the results. Would you help me to solve the problem?
Hi Maryam,
It could be a technical problem. Maybe you will need to write to [email protected] and they should help you.
Best!
Does anybody know that how I can make a biopython library for molecular dynamics modeling?
dear Ratih kusuma Wardani
please visit the below links:
1)
http://mmb.irbbarcelona.org/MDWeb/help.php?id=software
2)
http://haddock.science.uu.nl/enmr/services/GROMACS/server_full.php
3)
http://haddock.science.uu.nl/enmr/services/GROMACS/server_partial.php
you note that the above links need to user and password. you should make an account in those.
In also by using the below code in biopython you should make a model for your structure:
a) load a modeller in python by :
from modeller import *
b) Load the automodel class:
from modeller.automodel import *
c)request verbose output:
log.verbose()
d)create a new MODELLER environment to build this model in:
env = environ()
and etc.
you can test it!
for more help you can connect with me.
+989385436058
Hi,
MD Web allow you to run simulations up to 500 ps on server.
Also if you have issues on downloading the files, you might try disable the 'pop-up blockage' for your browser.
Hope it works!
Hi,
There is an online webserve "Molecular Dynamic on Web" which is just for preparing MD files for sure about accuracy of your system and you could do npt , nvt and energy minimization steps but could not run whole MD run.
http://mmb.irbbarcelona.org/MDWeb/index.php
I don't think, you could find an online Webserver for run whole simulation of a system.
Good luck.
Dear Ratih
I highly recommend you for using Gromacs package. I've performed several projects with this tool and I think it was a flexible and high quality simulation tool. There are several problems with web servers for MD simulation. For example they act only in default mode and you can not set a bunch of options for your simulation. Learning Gromacs is very easy and I think you can learn it as well as a web server.
Best,
Hassan
For simple tasks, try Chimera. It will solve most of your problems and you can run it on a PC with a good graphics card (2GB VRAM dedicated).
For complicated systems, forget about MD on the web. You get a total server space of 2 GB and a project space of 100 MB. It is too small to run MD of proteins.
As a suggestion, ask your IT guys to setup your own MD server with Gromacs. Servers are dirt cheap and you can get NVIDIA 1060+ card for under $200. It is sufficient to run 2 ns MD on a small protein with a shell water (T3P) within a week.
I don't have the facilities to run protein ligand complex in gromacs for MD Simulation for 30ns/50ns. Is there any free online software or server which can be used by payment. can anyone help me, please
Get NAMD installed on a paid server (cloud) and pay for the time you use the server. Please look up Penguin Computers or any other provider. There is plenty of those and you can get them to help you install the software.
I do not recommend AWS for security reasons. You may think differently if you want to stay with Linux and can install the software yourself.
Hello,
You can run your MD simulations by simply using a web-based tool named- CABS-Flex 2.0. Though, it runs on a 10nm scale, but, many researchers have used it for accomplishing MD tests.
Here is the URL of the tool: http://biocomp.chem.uw.edu.pl/CABSflex/
I have also used the tool and it is user-friendly. It may take about a day or two to get your results, but I think that is fine.
All the best!
Regards
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