Re: Few doubt on the numbers implying in REMD simulation

From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Tue Apr 12 2016 - 10:00:21 CDT

Hi Nicholus,

I am guessing you didn't get a response simply because this has been
explained very clearly in the replica exchange manual/tutorial. If you look
carefully through it, you will find what each of the variables specific to
REMD simulations mean, and from that, it will be trivial to calculate what
value you need to set to each variable to get a REMD simulation of a
specific length and a specific frequency of exchange attempt.

Hope this helps,
Chitrak.

On Tue, Apr 12, 2016 at 8:06 AM, Nicholus Bhattacharjee <
nicholusbhattacharjee_at_gmail.com> wrote:

> Hello all,
>
>
> I am puting this for the third time hoping for an answer.
>
> Hello all,
>
> I am using following values for my REMD calculations.
>
>
> ###############################################################################
>
> %.conf file
>
> set num_replicas 42
> set min_temp 300
> set max_temp 600
> set steps_per_run 1000
> set num_runs 50000
> # num_runs should be divisible by runs_per_frame * frames_per_restart
> set runs_per_frame 1
> set frames_per_restart 10
>
> %.namd file
>
> timestep 1.0
>
> amber yes
> parmfile octa.top
> coordinates octa.pdb
>
> margin 10.0
> stepspercycle 100
> exclude scaled1-4
> 1-4scaling 0.4
> switching on
> switchdist 7.0
> cutoff 8.0
> pairlistdist 10.0
>
> langevin on
> langevinDamping 10.0
>
>
> ###############################################################################
>
> I suppose it will provide me 50 ns trajectory for each replica.
>
> I just wanted to know how many exchange attempt will this simulation do
> and how much Hamiltonian dynamics between exchange attempts. Are they 50
> and 1000 ps respectively?
>
> Thanks for the reply.
>

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