Re: [AMBER] Is this output OK from the hybrid remd?

From: Bongkeun Kim <>
Date: Fri, 17 Dec 2010 08:43:59 -0800

Quoting case <>:

> 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
Thank you.
Bongkeun Kim

AMBER mailing list
Received on Fri Dec 17 2010 - 09:00:06 PST
Custom Search