Hii,
Try to use CHARMMing (http://www.charmming.org/charmming/html/skeleton/) ontains an integrated set of tools for uploading structures, performing simulations, and viewing the results. A comprehensive list of all MD softwares/servres can be accessed here http://www.click2drug.org/index.html#Molecular%20Modeling.
Best wishes,
SB
If you are willing to know about the theory of MD Simulation, plenty of links and good books are the; just do Google.
In order to know how to run AMBER, GROMACS or CHARMM, you can type GROMACs tutorial (a link from bevan lab is good) or AMBER tutorial (a link from AMBER site), these are good.
Hope this help
Aditya
If I don't misunderstood you want tor run MD simulations online, right? If it is the case try http://mmb.irbbarcelona.org/MDWeb/ . If that you want is online resources, try GROMACS or NAMD, you can read the manuals, download the programs and use it easily.
Thank you very much for your answers, dear melchor your online link helps me thanq......
NAMD using CHARMM is a very good software for MDS. Different types of extensive Analyses are possible. Data handling is also manageable.
If you decide to use NAMD, I can guide you well. I have done three 12ns simulations and 4 different Analyses for 3 Protein-Ligand docked structures.
I am using AMBER now. AMBERTOOLS14 contains essential engine (SANDER) to run MD simulation for free. But the GPU accelerated MD engine (PMEMD) is not free. Unless you want to use GPU, AMBER should be a great solution for MD simulation. I have wrote some blogs for AMBER installment https://sunxiaoquan.wordpress.com/2015/02/15/install-ambertools14-with-mpi-in-ubuntu-14-10-64bit/.
NAMD is a free MD simulation program and VMD is a powerful post-simulation analysis software. See the link below:
http://www.ks.uiuc.edu/Research/namd/
For Molecular Dynamic Simulation, NAMD is a freely available software
VMD also freely available for visualization and MD analysis
http://www.ks.uiuc.edu/Research/namd/
You can also try fastest MD simulation package and analysis tools GROMACS. It is free and can be downloaded from www.gromacs.org
Try using WeNMR grid (https://www.wenmr.eu/). There you can find both Amber and Gromacs on a single platform. All you need to have ICGA certificate from Indian authority, which is easy to get.
https://en.wikipedia.org/wiki/List_of_software_for_molecular_mechanics_modeling
Hello I know this comes very late 2 years later to be precise :) we just launched an online platform for doing your molecular simulation that is easy and intuitive to use. For anyone interested you can check it out below
https://ioniclabs.io
Hello
https://www.rcsb.org/pdb/static.do?p=software/software_links/modeling_and_simulation.html
Good Luck.
Santhosh Kumar Pasupuleti
in this field trust me I searched for powerful online servers for free unfortunately I didn't find any powerful reliable.
but here is the best one I found and easy to work with and with a citation on their server, also they can provide Rmsd and Rmsf.
"SimpleRun allows the user to execute simple MD runs (equilibration + production) from a system built with SystemBuilder".
https://www.playmolecule.org/SimpleRun/
best regards
Hello Santhosh Kumar Pasupuleti
Unfortunatey, to the best of my knowledge you cannot find a proper full-fledged and powerful MDS server online. You do have few options, but they run on a smaller build scale. One of them is the python package CABS FLEx 2.0; but it can cost you a lot of time. Another alternative is PELE server, a web server for predicting the dynamic interactions between proteins and ligands. But if you wanna setup a proper MDS, you gotta use softwares such as GROMACS, AMBER, Desmond etc.
The links for the above mentioned servers are given below:
CABS FLEx 2.0:
http://biocomp.chem.uw.edu.pl/CABSflex2
PELE server:
https://pele.bsc.es/pele.wt
Hope it helps.
HI, Try using webgro from the link posted below. It is an online tool which uses gromacs for its protein simulations. Great tool which is free to use for protein simulations.
https://simlab.uams.edu/index.php
This software conducts both minimization and MD simulation upto 200ns. It is a recently developed tool from my university and going through few more updates.
Hello.
Yes but it has some issues only perfomes short simulation time
Check https://mmb.irbbarcelona.org/MDWeb/
Hello sir have you tried any of these? Which of them is turned out to be best let me know.
Pankaj Mishra Hello Sir. Please tell in detail about ICGA certification obtained from Indian authority. It will be really helpful for me as well as other readers.
Ok thanks, @Akshatha Ganne is web gro available for other user also except UAMS users
Yes, Webgro(https://simlab.uams.edu/index.php ) is freely available for all the academic users. You just have to go ahead and register using your academic email ID and you can submit your job.
@ Shraddha Sriraman Hi, is this software performed to use in protein only.
Depends upon the structure of protein, it usually take 2 days for normal protiens
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