Dear all,
Recently I'm involved in performing MD simulation using AMBER.
At the beginning, the atom coordinates are saved to mdcrd file in every 4fs(ntrw=2) time interval. Then for comparison, I save the atom coordinates into mdcrd file every 10ps(ntrw=5000). Other parts of the two MD simulations are all the same, and the only difference is the frequency of saving atom coordinates. But the conformation between the two simulation give huge difference. That from former protocol is far from the XRD structure at the end. But that from the latter is similar to the XRD structure.
This results shocks me, because the frequency of saving atom coordinates shouldn't affect to MD simuation. I've checked all the input files, they are the same, except options controlling the output such as 'ntwx'. The program I use is sander in AMBER10, AMBER03 is the force field by which I've adopted to perform simulation. My system is villin headpiece. Furthermore, explicit solvation model TIP3P is used.
The following is the two input file:
---The frequently-output input-------------
&cntrl
imin = 0,
irest = 1,
ntx = 5,
ntb = 1,
cut = 12.0,
ntc = 2,
ntf = 2,
tempi = 300.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 1.0,
nstlim = 5000, dt = 0.002
ntpr = 2, ntwx = 2, ntwr = 2
/
----------------------------------------
---The not-so-frequently-output input---
&cntrl
imin = 0,
irest = 1,
ntx = 5,
ntb = 1,
cut = 12.0,
ntc = 2,
ntf = 2,
tempi = 300.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 1.0,
nstlim = 2500000, dt = 0.002
ntpr = 5000, ntwx =5000 , ntwr = 5000
/
----------------------------------------
can someone give me some advice and help me out of the trouble?
Thank you very much in advance.
Jianing
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Received on Mon Apr 12 2010 - 04:30:02 PDT
