AMBER Archive (2008)

Subject: RE: AMBER: help MD running error

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri May 23 2008 - 10:30:03 CDT


Hi Qiuting,

 

You don't terminate the &dipoles namelist.

 

It needs to read:

 

 &dipoles

  dipole moment calculation

  RES 1 1

 END

 END

 /

 

Good luck,

 

Ross

 

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Qiuting Hong
Sent: Friday, May 23, 2008 1:40 AM
To: amber_at_scripps.edu
Subject: AMBER: help MD running error

 

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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