Re: User-defined forces in NAMD

From: Ali Ghaffaari (ali.ghaffaari_at_gmail.com)
Date: Wed Apr 11 2012 - 13:12:04 CDT

Dear Ehsan,

After a little search I found that you're right. LAMMPS is easier to
change. Thanks! ;)

Dear Axel,

The problem is clear for me. But I don't want to implement a simulator from
scratch! Besides, I've just started to study MD and I need time to be
experienced. Thanks for your advice!

On Tue, Apr 10, 2012 at 9:25 PM, Ehsan Ban <ehsan.ban_at_gmail.com> wrote:

> Hi,
>
> If you want to customize things I think it would be much easier to use
> LAMMPS.
>
> Bests
> EHsan
>
>
> On Tue, Apr 10, 2012 at 8:16 AM, Axel Kohlmeyer <akohlmey_at_gmail.com>wrote:
>
>>
>>
>> On Apr 10, 2012, at 7:38 AM, Ali Ghaffaari <ali.ghaffaari_at_gmail.com>
>> wrote:
>>
>> > Hello,
>> >
>> > I'm not skilled in MD. I have question about force field using NAMD. As
>> I read in a NAMD documentation, it's using five potential energies:
>> U(bond), U(angle), U(dihedral), U(vdW), and U(Coulomb). I want to simulate
>> a protein by using a custom potential function for each atom rather than
>> these five potential energies. How can I do that? Is it possible by using
>> NAMD? or other MD tools?
>>
>> To be able to properly do that you *first* have to become experienced in
>> MD. It is not a matter of the tool, but a matter of understanding. Starting
>> a project you don't understand is a recipe for disaster.
>>
>> Axel
>>
>>
>>
>>
>> >
>> > Thanks a lot,
>> > Ali
>>
>>
>

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