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 - 03:09:06 PDT
