If you apply accel only on the dihedral potential, you will consider of course all atoms that contribute to the dihedral potential (do DNA atoms contribute or not?). If you apply accel to the total potential, you will of course consider all atoms in your system as all contribute to the total energy.
I would also advise you to read the most recent papers from the McCammon group. They have recently (PNAS paper 2013) introduced a more intuitive way to define the parameters that uses a single variable lambda to define both parameters. Especially useful for mixed systems.
I also agree with what Jason said.
Best,
Vlad
Sent from my android device.
-----Original Message-----
From: Jason Swails <jason.swails.gmail.com>
To: Sourav Purohit <sour000.gmail.com>
Cc: AMBER Mailing List <amber.ambermd.org>, Ross Walker <ross.rosswalker.co.uk>
Sent: Sun, 27 Apr 2014 4:03 PM
Subject: Re: [AMBER] Accelerated MD
On Sun, Apr 27, 2014 at 7:01 AM, Sourav Purohit <sour000.gmail.com> wrote:
> Hi all,
>
> I had some doubts on the method of calculating parameters for accelerated
> MD as described in the AMBER12 manual (page no.160).
>
> 1.Does the total number of atoms (taken as 16950 in the example) include
> atoms belonging to water molecules also??
>
> 2.for the calculation of alphaD, only the number of protein residues goes
> as an input. What if a system has other components like DNA?? Should I
> include the DNA residues also??
>
> Kindly help.
>
> Thanks.
>
​Please do not double post and do not send copies of questions to our
private emails; it is inconsiderate (especially when asked on a weekend,
where people do not check emails as frequently). The reason you have not
received an answer is either:
1) Nobody knows the answer
2) Someone that does know the answer has not yet had the time to answer.
In either case, please exercise patience and wait for someone to answer.
Thanks,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Apr 27 2014 - 07:30:02 PDT
