I studied, plant metabolites on different target proteins involved in diabetes. I have done docking using MGL tools. Now, I want to study simulation of the candidate molecule.
If there any free simulation servers available in online?
I am presuming you are referring to MD (or MM type simulations) if not please elaborate upon your question.
Most Web based options are going to be just for preparation and analysis. Full motion simulations, especially with explicit water, become very cycle intensive quickly, thus are set up on high compute systems.
Most existing pre-setup systems available to researchers at none to low cost exist within schools or as national/international collaborations to which you will have to apply to, to get access.
this include (but are not limited to) https://www.wenmr.eu, http://www.opensciencegrid.org/, https://www.xsede.org/) eligibility criteria vary.
Other groups like Google exacycle and amazon cloud will give you research grants and academic usage discounts.
PS if you are interested, and have some experimental data to go with it I may be able to set you up with a run or so as a low level collaboration on
Looks like you can run http://www.acellera.com/support/documentation/ which includes Amber, Charmm and OPLS force fields, at https://aws.amazon.com/marketplace/pp/B00Q5ECSOG