I've used the ATB, there kinda the replacment for the PRODGR, which is now commercial. They do have the same problems though, such as 99% correct output, and then manual changes for something (example: an NH2 on the side of a ring parameterized as an NH3, so acts as such...needs to be changed, but you may not notice it until short simulations are run, with all other atoms out of 30-40 correct...).
Stephan Watkins
Gesendet: Dienstag, 03. Dezember 2013 um 12:17 Uhr
Von: "Hardy, Adam" <ah...@hw.ac.uk>
An: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org>
Betreff: Re: [gmx-users] Atomistic Simulation
Von: "Hardy, Adam" <ah...@hw.ac.uk>
An: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org>
Betreff: Re: [gmx-users] Atomistic Simulation
I've just started doing atomistic simulations over the last few weeks as well and can share what I've learned so far.
I have been using 'automated topology builder'. It only uses the gromos 53a6 forcefield so eliminates the choice if you want to use it. ATB generates the pdb and itp files for you. There are a lot of molecules already on there or you can submit you're own using a _javascript_ molecule builder.
There may well be other ways to do this but I haven't found them yet.
On 3 Dec 2013 10:14, panzu <sergio.panzu...@estudiante.uam.es> wrote:
Hello to everybody,
I am new in atomistic simulations and a have some doubts about how to do it.
I wanna simulate a mixture of Cyclohexane, Toluene and Dodecane.
My questions are, ¿Where do I get the pdb files of these molecules
from? and ¿How do I know which force field I should choose in pdb2gmx
in order to make the itp file?
Thanks in advance,
Panzu
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I have been using 'automated topology builder'. It only uses the gromos 53a6 forcefield so eliminates the choice if you want to use it. ATB generates the pdb and itp files for you. There are a lot of molecules already on there or you can submit you're own using a _javascript_ molecule builder.
There may well be other ways to do this but I haven't found them yet.
On 3 Dec 2013 10:14, panzu <sergio.panzu...@estudiante.uam.es> wrote:
Hello to everybody,
I am new in atomistic simulations and a have some doubts about how to do it.
I wanna simulate a mixture of Cyclohexane, Toluene and Dodecane.
My questions are, ¿Where do I get the pdb files of these molecules
from? and ¿How do I know which force field I should choose in pdb2gmx
in order to make the itp file?
Thanks in advance,
Panzu
--
View this message in context: http://gromacs.5086.x6.nabble.com/Atomistic-Simulation-tp5012984.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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Fourth university in the UK and top in Scotland (National Student Survey 2012)
We invite research leaders and ambitious early career researchers to
join us in leading and driving research in key inter-disciplinary themes.
Please see www.hw.ac.uk/researchleaders for further information and how
to apply.
Heriot-Watt University is a Scottish charity
registered under charity number SC000278.
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