AMBER Archive (2009)

Subject: Re: [AMBER] AMBER job restart problem

From: Kefa Lu (kefa.lu_at_gmail.com)
Date: Sun Aug 16 2009 - 00:09:22 CDT

OK. Thanks a lot!

Kefa

Thomas Cheatham wrote:
>> Thanks a lot! Dr. Cheatham. If I run constant (isotropic) pressure
>> simulation, will the situation be better? My system is a lipid bilayer
>>
>
> The same.
>
>
>> Another question is, if I don't use the original refc restraint
>> coordinates all the time, but change it every time when restart the
>> simulation, then the structure of the restraint part of the system might
>> change too much if I restart the simulation too many times, right? Will
>>
>
> Yes, but the change is small. If you are restraining a single large
> protein, what is happening as it runs is that the center of mass (assuming
> the default of NSPCAL=1) of the protein is shifting. Using the previous
> restart will have the shift, but the coordinates will not have changed so
> much. If you are restraining multiple molecules, this is a larger issue
> which can iterate offline.
>
>
>>>> GRP1
>>>> 100.0
>>>> ATOM 1 13609
>>>>
>
> Again, drop the force constants to 5-15 kcal/mol. This will still highly
> restrain atoms 1 13609 yet avoid the need for vlimit restrictions.
>
> --tom
>
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