I'm not sure if this is the cause of the problem, but you might
want to make sure you are removing center of mass rotation
and translation.
----- Original Message -----
From: "Soonmin Jang" <sjang_at_protege.snu.ac.kr>
To: <amber_at_heimdal.compchem.ucsf.edu>
Sent: Tuesday, September 10, 2002 6:09 AM
Subject: Strange MD simulation results with GB solvation at high temp.
> Hello,
>
> I posted this mail previously but somehow it seems it is not delivered
> correctly. So, here I post it again.
>
> I am running MD with GB solvation (generalied Born). The system is very
simple.
> It is Met-Enkephlain { ACE TYR GLY GLY PHE MET NME }.
> It runs OK up to several nano seconds. But it shows very strange behavior
> after several naosecond (about 3 ns for in this case).
> There begin to appear large temperature and energy fluctuation and the
> energy distribution is NOT Boltzman anymore after this point.
>
> Here is the temperature profile as time step. (30000 corresponds to 3.0
ns).
>
> 1000
++-------+--------+-------+--------+--------+--------+-------+-------++
> + + + + + +
+'bb.dat'******* +
> | * ** *** ****
|
> 900 ++ ********
*****++
> |
************** |
> |
************** |
> 800 ++
***************++
> | ** * * * *
**************** |
> ************** **** *
*********************************************** |
> 700
*********************************************************************++
>
********************************************************************* |
> 600
*********************************************************************++
>
********************************************************************* |
>
********************************************************************* |
> 500
*********************************************************************++
> | * *** * * * *** * ******** * * * *
******************* |
> | * *
*************** |
> 400 ++
**************++
> | *************
|
> + + + + + + + *+
+
> 300
++-------+--------+-------+--------+--------+--------+-------+-------++
> 0 5000 10000 15000 20000 25000 30000 35000
40000
>
>
> Ans here is the run script I used
>
> &cntrl
> ntb=0, igb=1, ig=17436,
> imin=0, irest=0, ntx=1, tempi=300.0, ntt=1, temp0=604.0, tautp=0.5,
> nstlim=4000000, dt=0.001,
> ntwe=100, ntwx=500, ntpr=5000,
> &end
>
> Any comments will be appreciated.
> Thank you.
>
> Soonmin
>
>
>
Received on Tue Sep 10 2002 - 05:07:58 PDT
