[gmx-users] request

[leila separdar]

hi
do I need any .pdb file for making .gro and .top file?

I make .pdb  file with hyperchem software and then I used pdb2gmx command in
order to make .gro and .top files. but I think my way is wrong. is it true?

is there anybody that done this simulation?
leila





On Sun, Nov 21, 2010 at 11:24 AM, Amit Choubey <kgp.amit at gmail.com> wrote:

> Hi,
>
> Define an itp file which has the non-bonded info. Then define a mdp (md
> parameter file) and also make a structure file (gro). Also you need a
> topology file (top) which corresponds to the structure file.
>
> You will have to do some background work. Manual should be your friend.
>
> amit
>
>   On Sat, Nov 20, 2010 at 11:32 PM, leila separdar <
> separdar.leila at gmail.com> wrote:
>
>>   I am beginner with gromacs. I would like to simulate the behavior of
>> glassy materials starting with simple Lennard Jones liquid.
>> please advise me as to how to begin.
>> a relevent flowchart or tutorial would be of immerse help
>> thank you very much indeed.
>>
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>
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