Hello,
Is it possible to have constant pressure (e.g. 1 atm) in GB simulation? I have
minimized the protein-ligand complex. In the equilibration, the system was
heated up to 300K. In output file:
NSTEP = 3450 TIME(PS) = 6.900 TEMP(K) = 292.00 PRESS = 0.0
Etot = -3476.7635 EKtot = 3804.4867 EPtot = -7281.2502
BOND = 937.6709 ANGLE = 2315.2862 DIHED = 3282.1783
1-4 NB = 1326.5105 1-4 EEL = 13682.1958 VDWAALS = -2482.9081
EELEC = -21886.4208 EGB = -5767.0078 RESTRAINT = 1235.6113
ESURF = 75.6335
EAMBER (non-restraint) = -8516.8615
It looks like the pressure in my system is 0 atm. I think it's wrong.
Here is my input file for equlibration.
&cntrl
imin = 0,
ntc = 2, ntf = 2,
cut = 12.0, igb = 2, saltcon = 0.002, gbsa = 1,
ntpr = 50,
nstlim = 10000, dt = 0.002,
ntt = 1, tempi = 100.0, temp0 = 300, taup = 1.0,
ntx = 1, irest = 0, ntb = 0,
nscm = 1000,
ntr = 1,
&end
keep all atom frozen
5
RES 1 328
END
END
What might be the problem?
Thanks in advance.
aini
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Received on Thu Oct 02 2003 - 02:53:00 PDT
