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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