Dear amber,
I am trying to run proline in explicit water and print out the dipole
information. my input file is as follows:
pro_water_md2: run MD at 300temp
&cntrl
imin =0, irest =1, ntx =7,
ntb =2, pres0 =1.0, ntp =1,
taup =2.0,
cut =5.0, ntr=0,
ntc =2, ntf =2,
tempi =300.0, temp0 =300.0,
ntt =3, gamma_ln =1.0,
nstlim =20000000, dt =0.002,
ntpr =500, ntwx =500, ntwr =1000
/
&dipoles
dipole moment calculation
RES 1 1
END
END
However, for some reason, the MD stops at the first step. Here is the result
amber gives me:
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
---------------------------------------------------
APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
using 5000.0 points per unit in tabled values
TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.2763E-14 at 2.626100
| CHECK d/dx switch(x): max rel err = 0.7759E-11 at 2.814040
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 63613
| TOTAL SIZE OF NONBOND LIST = 63613
NSTEP = 500 TIME(PS) = 21.000 TEMP(K) = 303.43 PRESS =
-1936.0
Etot = -2969.8593 EKtot = 709.7007 EPtot =
-3679.5600
BOND = 1.4874 ANGLE = 10.8486 DIHED =
5.4603
1-4 NB = 0.7505 1-4 EEL = 40.6799 VDWAALS =
478.1974
EELEC = -4216.9841 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 354.1798 VIRIAL = 972.9917 VOLUME =
14803.4972
Density =
0.7953
Ewald error estimate: 0.1254E-01
------------------------------------------------------------------------------
------------------------------- DIPOLE INFO
----------------------------------
NSTEP = 500 TIME(PS) = 21.000
rfree: End of file on unit
-----------------------------------------------------
*Does anybody know what happen here? I am using AMBER 8.*
Qiuting
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Received on Sun May 25 2008 - 06:07:46 PDT
