Quoting case <case.biomaps.rutgers.edu>:
> On Fri, Dec 17, 2010, Bongkeun Kim wrote:
>>
>> I just run the hybrid remd and checked the output file.
>> It said ********** on EPot. Does it mean only the number is too big to
>> print or is there any problem on this run?
>
> There seems to be a problem with the restraint energy:
>
>> EELEC = -6589.2279 EGB = -3004.6220 RESTRAINT
>> =57092146.9150
>
> You can't run replica exchange simulations with ntr>0 (unless, I guess, that
> all replicas have the same reference structure. Also, be sure that you can
> sucessfully run non-exchange simulations at each temperature of interest.
>
I already tried to run it with full explicit water and it gave me no
problem. But this run demands too many resources.
With hybridgb, EPtot = 58053860.3203 and
Without hybbridgb, EPtot = 546283.2545.
Also, RESTRAINT = 57444151.6840 with hybridgb and
RESTRAINT = 177.4334 without hybridgb.
It seems like the hybridgb method overestimates restraint energy of my
graphite surface too much. I checked the structure of whole system.
The peptide lies on the graphite surface now. I think explicitly
considered water molecules by numwatkeep=500 are on the other side of
graphite surface, that is across the surface. Do you think this makes
problems?
Thank you.
Bongkeun Kim
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Received on Fri Dec 17 2010 - 09:00:06 PST
