RE: AMBER: help MD running error

From: Ross Walker <ross.rosswalker.co.uk>
Date: Fri, 23 May 2008 08:30:03 -0700

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.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Qiuting Hong
Sent: Friday, May 23, 2008 1:40 AM
To: amber.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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Received on Sun May 25 2008 - 06:07:53 PDT
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