Dear All,
I have run MD using SANDER_CLASSIC with input;
-------------------
equil_step 1 dynamics step 1, 25 kcal/mol.A solute restraint
&cntrl
ntx = 1, irest = 0, nmrmax = 0,
imin = 0,
maxcyc = 1000, ncyc = 5000,
ntmin = 1, dx0 = 0.01, dxm = 0.5, drms = 0.0001,
nrun = 1,
nstlim = 30,
dt = 0.002, init = 3, t = 0.0,
timlim = 999999., ndfmin = 0, ntcm = 0, nscm = 0,
ntpr = 10, ntwr = 30,
ntwprt = 0, ioutfm = 0, ntrx = 1, ntxo = 1,
cut = 9.0, ntnb = 1, nsnb = 10, ntid = 0,
scnb = 2.0, scee = 1.2, cut2nd = 0.0, ichdna = 0,
idiel = 1, dielc = 1.0,
ntb = 2, ntp = 1, npscal = 1,
pres0 = 1.0, comp = 44.6, taup = 0.2,
ntc = 2, tol = 0.0005,
ntf = 2,
ibelly = 0, ntr = 1,
temp0 = 300.0, tempi = 300.0,
ig = 71277, heat = 0.0,
ntt = 1, isolvp = 0, dtemp = 0.0,
tautp = 0.2, tauts = 0.2, vlimit = 20.0,
tauv0 = 0.0, tauv = 0.1, vzero = 0.0,
isftrp = 0, rwell = 0.0,
ipol = 0,
imgslt = 0, iftres = 1,
jfastw = 0,
ivcap = 0, matcap = 0, fcap = 1.5,
iewald = 1,
&end
46.2573613 45.0369329 57.8298522 90.0000000 90.0000000 90.0000000
48 48 60 4 0 0 0
0.00001
Constraints
25.0
RES 1 20
END
END
=======================
and I tried to modify this input to run with SANDER by deleting some
variables
which were not defined in SANDER, as following
----------
equil_step 1 dynamics step 1, 25 kcal/mol.A solute restraint
&cntrl
ntx = 1, irest = 0, nmropt = 0,
imin = 0,
maxcyc = 1000, ncyc = 5000,
ntmin = 1, dx0 = 0.01, dxm = 0.5, drms = 0.0001,
nstlim = 30,
dt = 0.002, t = 0.0,
timlim = 999999., ndfmin = 0, ntcm = 0, nscm = 0,
ntpr = 10, ntwr = 30,
ntwprt = 0, ioutfm = 0, ntrx = 1, ntxo = 1,
cut = 9.0, nsnb = 10,
scnb = 2.0, scee = 1.2,
dielc = 1.0,
ntb = 2, ntp = 1, npscal = 1,
pres0 = 1.0, comp = 44.6, taup = 0.2,
ntc = 2, tol = 0.0005,
ntf = 2,
ibelly = 0, ntr = 1,
temp0 = 300.0, tempi = 300.0,
ig = 71277, heat = 0.0,
ntt = 1, dtemp = 0.0,
tautp = 0.2, vlimit = 20.0,
ipol = 0,
jfastw = 0,
ivcap = 0, matcap = 0, fcap = 1.5,
igb = 0, gbparm = 2, readrad = 0,
offset = 0.09, igbfreq= 1, gbsa = 0,
surften= 0.005,
&end
&ewald
a = 46.2573613, b = 45.0369329, c = 57.8298522,
alpha = 90.000, beta = 90.000, gamma = 90.000,
nfft1 = 48, nfft2 = 48, nfft3 = 60,
order = 4, dsum_tol = 0.00001,
&end
Constraints
25.0
RES 1 20
END
END
======================
I obtained the SANDER result which quite different from SANDER_CLASSIC
result and
running SANDER toke cpu time more than running SANDER_CLASSIC.
Could anyone help me to modify input for SANDER to obtain the
corresponding result with SANDER_CLASSIC?
Thank you very much.
Sincerely yours,
Khatcharin
Received on Thu Mar 08 2001 - 10:18:44 PST
