Dear all£¬
I¡¯m now setting up a system used Explicit solvent pH-REMD methods.
Now I¡¯ve equilibrate the system following Jason swails¡¯s input
(
http://jswails.wikidot.com/explicit-solvent-constant-ph-md). Thanks for
Jason¡¯s website very much first.
And in the production part, I want to relax my system in different pH, later
the REMD will be used in my system. So I submitted a job with the parameter
rem -0
-O -rem 0 -i equilibrate.mdin.001 -o equilibrate.mdout.001 -c HdeB.
equil.rst7 -r equilibrate.rst.001 -x equilibrate.nc.001 -inf
equilibrate.mdinfo.001 -p HdeB.mod0.parm7 -cpin HdeB.cpin -cprestrt
equilibrate.cpin.001 -cpout HdeB_equil.cpout.001
-O -rem 0 -i equilibrate.mdin.002 -o equilibrate.mdout.002 -c
HdeB.equil.rst7 -r equilibrate.rst.002 -x equilibrate.nc.002 -inf
equilibrate.mdinfo.002 -p HdeB.mod0.parm7 -cpin HdeB.cpin -cprestrt
equilibrate.cpin.002 -cpout HdeB_equil.cpout.002
¡
My system contains 158AA, and the box size is about 60A wide.
And this is one of my input
Explicit solvent constant pH MD
&cntrl
imin=0, irest=1, ntx=5, ntxo=2,
ntpr=1000, ntwx=1000, nstlim=1000000,
dt=0.002, ntt=3, tempi=300,
temp0=300, gamma_ln=5.0, ig=-1,
ntc=2, ntf=2, cut=10, iwrap=1,
ioutfm=1, icnstph=2, ntcnstph=100,
solvph=3, ntrelax=100, saltcon=0.1,
/
But I find that my result is a bit strange,
NSTEP = 25000 TIME(PS) = 4450.000 TEMP(K) = 300.53 PRESS =
0.0
Etot = -42092.0788 EKtot = 11035.7300 EPtot =
-53127.8088
BOND = 483.2164 ANGLE = 1414.5800 DIHED =
1814.3705
1-4 NB = 568.2945 1-4 EEL = 7579.1143 VDWAALS =
5700.8533
EELEC = -70688.2377 EHBOND = 0.0000 RESTRAINT =
0.0000
Ewald error estimate: 0.8623E-02
----------------------------------------------------------------------------
--
wrapping first mol.: -40.77263 28.83061 49.93608
wrapping first mol.: -40.77263 28.83061 49.93608
NSTEP = 26000 TIME(PS) = 4452.000 TEMP(K) = 263.77 PRESS =
0.0
Etot = -43266.8387 EKtot = 9686.1128 EPtot =
-52952.9515
BOND = 475.0383 ANGLE = 1457.7215 DIHED =
1807.6935
1-4 NB = 585.0764 1-4 EEL = 7580.6866 VDWAALS =
5623.4670
EELEC = -70482.6348 EHBOND = 0.0000 RESTRAINT =
0.0000
Ewald error estimate: 0.8918E-02
The Ewald error estimate is roughly too high and the temperature is unstable
here.
I want to know why and how to change my parameter.
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Received on Wed Jul 22 2015 - 08:00:03 PDT
