Re: [AMBER] REMD equilibration restart

From: Sangita Kachhap <>
Date: Mon, 31 Jan 2011 22:09:29 +0530 (IST)

Hello carlos

I am doing a trail run for REMD I have taken 8 replicas minimum temperature is
and maximum is 492.7
I have am running two REMD one for phosphorylated and second for unphosphorylated.
I am equlibrating it for 1ns. Unphosphorylated ran successfully but phosphorylated
stopped after ~800ps without any error i think its a cluster error.

Now I want to know can I restart equilibration where it has stopped?

Since equilibration run stopped at final temperature and if I restart
here it is not clear to me how I define the temp0 and tempi in
equilibration.medin file.

Here it is not clear to me

I think you got what I want to say.

> it isn't clear to me what you are doing or asking. can you try explaining in
> more detail? you need to tell us how you determined the temperature spacing
> of the replicas. Is the problem that there are no exchanges? or that it
> stopped? and what do you mean by "stopped"?
> On Sun, Jan 30, 2011 at 2:45 AM, Sangita Kachhap <>wrote:
>> Hello all,
>> I am runing REMD, first I was equilibrating it for 1ns but it stoped after
>> ~835ns.
>> I am runing tow separate REMD for am amino acid (one as refrence) in my
>> protein
>> one is runing still.
>> Since in equilinration there is no exchange of replica, So can I restart
>> equlibration from where it has stoped?
>> Can please anybody suggest me?
>> With regard
>> Sangita Kachhap
>> JRF
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Sangita Kachhap

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Received on Mon Jan 31 2011 - 09:00:02 PST
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