[gmx-users] Md simulation by Gromacs

[Erik Marklund]

Dear Maria,

Let’s keep this to the user list. I am first of all not a private tutor. Secondly, the answers you get (below) might be relevant for others.

> On 6 Apr 2017, at 16:04, maria khan <mariabiochemist1 at gmail.com> wrote:
> 
> Good evening Dear sir Erik Marklund..
> 
> I am very Thankful for your attention ..Actually i even dont know the basics and one of the NAMD expert user told me so that gromacs use united atom ff thats why gromacs is fast and NAMD use all atom thats why it is slow.
> 

That is incorrect. Gromacs can do both all-atom and united-atom. Gromacs can also make use of virtual sites, which allows for a longer time step, hence more simulated ns per hour. You can also choose not to. And then there are on top of that a number of reasons why gromacs is really fast without cutting (important) corners.

> Now my problems are : is there any option for considering hydrogen atom  to process its calculation in MD run as last time when i did simulation i applied the command of ignoring hydrogen atom ,,secondly what is the difference Between ignoring h- atoms and considering it in MD running.I mean would it effect the result of calculation after MD run..and if there is option for taking h- atom as part of amino acid then why there is an option for ignoring it..
> 

Please be specific. Are you referring to pdb2gmx -ignh? That just tells pdb2gmx to derive hydrogen positions and occupancies based on hydrogen bonding patterns and force-field-related information. It doesn’t normally produce topologies without hydrogens, and the hydrogens are thus part of the subsequent simulations. See the user-list archives. I know this has been discussed before. And you can also inspect the output files to see what they contain.

> Furthermore i dont know about forming parameters for my ligand thats is alkaloid so im confuse how to form its parameter and if some one has published its parameters then how i can find..i just need a stepwise protocol for MD simulation,,most of the manuals are not understandable my majors are pure biochemistry and mostly the explanations there are mathematica basedl.
> 

Well, parametrisation is not really for beginners. I also think others are more experienced in that area than I am.

> And yes i have studied the old version of manuals not updated one.
> 
> IF u have simplist form of manuals or any other stuff, kindly send me that i very thankful. Last time u shared a paper of ur self but it was not my research related.
>