Dear all,
I am trying to get the free energy caused by 2 arginine mutations in a
60 residue protein. To have more control over the course of simulation I
am following a 3 step procedure as described in the tutorial 9. My
question is about the charge removal part, I am removing the charges on
the whole softcore region which is composed of side chains of the 2
arginines and the 2 counter ions that are not present in mutant system
(V1). Is it normal to have large DV/DL numbers like this?
Etot = -44404.9050 EKtot = 11028.0591 EPtot = -55432.9641
BOND = 169.7565 ANGLE = 456.8468 DIHED = 631.1784
1-4 NB = 215.1196 1-4 EEL = 1808.0657 VDWAALS =
7920.2721
EELEC = -66634.2033 EHBOND = 0.0000 RESTRAINT =
0.0000
DV/DL = 464.5739
EKCMT = 5164.4127 VIRIAL = 5044.5572 VOLUME = 363040.4469
Density =
0.5075
Ewald error estimate: 0.1197E-03
mdin:
NPT production
&cntrl
imin = 0, ntx = 5, irest = 1,
ntpr = 1000000, ntwr = 100000, ntwx = 10000,
ntf = 1, ntc = 2, noshakemask=':64,65,23,43 & !
(.CA,C,N,O,H,H1,H2)',
ntb = 2, cut = 12.0,
nstlim = 100000, dt = 0.001,
temp0 = 300.0, ntt = 3, gamma_ln = 20,
ntp = 1, pres0 = 1.0, taup = 2.0,
icfe=1, clambda = 0.1,
ifsc=0,
crgmask='',
&end
Thank you in advance,
Elif
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Received on Fri Dec 28 2012 - 16:00:02 PST
