AMBER Archive (2008)

Subject: AMBER: help MD running error

From: Qiuting Hong (qiutinghong_at_gmail.com)
Date: Fri May 23 2008 - 03:40:12 CDT

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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