Dear Sangita,
I cannot help you with the amber input files, but you need much more
replicas if you want to have a temperature range of almost 250 K! The
temperature distributions of two neighbouring replicas must overlap.
This is a nice webserver to predict the temperatures:
http://folding.bmc.uu.se/remd/index.php
Good luck,
Nadine
------------------------------------------------------------
Dr. Nadine Utz
Molecular Modelling & Bioinformatics Group
Institute for Research in Biomedicine (IRB) Barcelona
Sangita Kachhap wrote:
> Hello carlos
>
> I am doing a trail run for REMD I have taken 8 replicas minimum temperature is
> 252.8
> 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
> equilibration
> 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 <sangita.imtech.res.in>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
>>> BIC,IMTECH
>>> CHANDIGARH
>>>
>>>
>>> _______________________________________________
>>> 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
>>
>>
>
>
> Sangita Kachhap
> JRF
> BIC,IMTECH
> CHANDIGARH
>
>
> _______________________________________________
> 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 Mon Jan 31 2011 - 09:30:05 PST
