This is the code from repl_ex.c important for your question:
In the function get_replica_exchange:
m= (step / re->nst) %2;
#re->nst=number of steps that you give with the -replex option
for(i=1; i<re->nrepl; i++) {
a = re->ind[i-1];
b = re->ind[i];
bPrint = (re->repl==a || re->repl==b);
if (i % 2 == m) {
check for exchange
}
When step/re->nst is odd m is 1 result is the e.g. for a system with 3
replicas and a swap attempt every 500 steps:
step500 0 x 1 2
step1000 0 1 x 2
step1500 0 x 1 2
etc...
So when step/re-nst is odd exchange is attempted between odd replicas
and odd replica -1, when step/re-nst is even exchange is attempted
between even replica and even replica -1.
hope this helps,
servaas
On Tue, 2008-11-25 at 10:05 +0100, [EMAIL PROTECTED] wrote:
> ------------------------------
>
> Message: 5
> Date: 25 Nov 2008 09:05:35 -0000
> From: "sarbani chattopadhyay" <[EMAIL PROTECTED]>
> Subject: [gmx-users] how many pairs are exchanged in replica exchange
> To: "gmx_users" <[email protected]>
> Message-ID: <[EMAIL PROTECTED]>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> Hi,
> I am new to Replica exchange molecular dynamics.
> I obtained the optimal temperature distribution based on the
> lowest and highest
> tempearture and exchange probability from the REMD caclulator ,
> available through the
> gromacs homepage.
> There were 17 temperaure values as output. I prepared 17 ".tpr" files
> based on the
> temperatures.
> What I want to know is that at each attempted step of replica
> exchange, how many pairs of
> replicas will be exchanged, and how this is decided?
>
> Thanks in advance,
> Sarbani
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