Dear Sir/Madam,
I could like to do the umbrella sampling simulation for a drug moving away
from the receptor,
and then do the PMF based on the distance (along 1D axis) between the drug
and receptor.
I could like to vary the distance betweent the drug and the receptor, i.e.
the drug move
in the 1D axis, i.e. keep the angles between the receptor and drug constant.
It is how I write the input files:
=============================================================
In file is written as:
Production MD
&cntrl
imin=0, saltcon=0.5
nstlim=5000, dt=0.002, ntc=1, ntr=1,
ntpr=100, ntwx=100,
cut=16, ntb=0, igb=1,
ntt=3, gamma_ln=1.0,
tempi=300.0, temp0=300.0,
/
&wt type='DUMPFREQ', istep1=10 /
&wt type='END' /
DISANG=1.restraint
DUMPAVE=1.result
END
=============================================================
=============================================================
1.restraint is written as:
# vary distance restrainst
&rst iat=4,5, r1=0.0, r2=1.0, r3=1.0, r4=100.0, rk2 =60.0, rk3 = 60.,
iresid=1,
ATNAM(1)=P,
ATNAM(2)=N10, ATNAM(2)=N12 /
# fixed angle restrainst
&rst iat=4,5,5 r1=-180.0, r2=180.0, r3=180.0, r4=180.0, rk2 = 1000.0, rk3 =
1000., iresid=1,
ATNAM(1)=P,
ATNAM(2)=N10,
ATNAM(3)=O18/
# fixed torsional angle restraint
&rst iat=4,5,5,5 r1=0.0, r2=0.0, r3=0.0, r4=360.0, rk2 = 1000.0, rk3 =
1000.0, iresid=1,
ATNAM(1)=P,
ATNAM(2)=N10,
ATNAM(3)=N12,
ATNAM(4)=O18/
=============================================================
I repeat the calculations by changing the r2/r3 to other values upon to 40
A.
However, most of the MD clashed finally or, both angles changed frequently.
It tried to use a smaller rk2 and rk3 values for the fixed angle and
torisional angle, e.g. 60.0 or 30.0.
What is the best way to fix two of the angles while changing the distance?
Best regards
Cat
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Received on Sun Jun 10 2007 - 06:07:23 PDT
