Thanks Nadine for reply and for the link to predict temperature.
Thanks once again.
> 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
>>>>
>>>>
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>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>>
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>>>
>>>
>>
>>
>> Sangita Kachhap
>> JRF
>> BIC,IMTECH
>> CHANDIGARH
>>
>>
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
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>
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
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Received on Mon Jan 31 2011 - 19:30:08 PST
