AMBER Archive (2009)

Subject: [AMBER] Calculaiton stop ?

From: xuemeiwang1103 (xuemeiwang1103_at_163.com)
Date: Thu Nov 05 2009 - 07:11:31 CST

Hi:
    I have sucessfully heated my protein system to 300K in 45ps .Then production of 5000ps were carried out at physilogical conditions (300k 1atm) in the NPT ensemble.But the odd thing is that the calculation often stopped with nothing seems wrong ,for example,it may calculate just 10ps then stopped.So I have to use the sander command again and again to let the computer continue the calculation.Until now ,I couldn't find there is something wrong about my system by viewing the structure of my protein sysytem.I am rather puzzeled with this phenomenon.Could someone kind enough to tell me the reaon why the calculation often stop,is it mean there is something wrong with my innitial system ?Thank you very much!
   hear is my inputfile which I used again and again:
Stage equilibration of qqup
&cntrl
 imin=0,irest=1,ntx=5,
 ntb=2,pres0=1.0,ntp=1.0,taup=2.0,
 cut=8.0,ntr=0, nmropt=1,
 ntc=2,ntf=2,
 tempi=300.0,temp0=300.0,
 ntt=3,gamma_ln=1.0,
 nstlim=2500000,dt=0.002,
 ntpr=500,ntwx=500,ntwr=1000
/

&wt type='END' /
LISTOUT=RST.out
DISANG=dis.RST
.........

the out :

NSTEP = 5500 TIME(PS) = 259.000 TEMP(K) = 302.29 PRESS = -13.2
 Etot = -198802.0760 EKtot = 49983.3473 EPtot = -248785.4233
 BOND = 1817.6782 ANGLE = 4915.1382 DIHED = 3517.3923
 1-4 NB = 2132.7487 1-4 EEL = 23974.2329 VDWAALS = 27867.6470
 EELEC = -313010.2606 EHBOND = 0.0000 RESTRAINT = 0.0000
 EKCMT = 21595.2523 VIRIAL = 21825.1955 VOLUME = 807615.7072
                                                    Density = 1.0217
 Ewald error estimate: 0.9172E-05
 ------------------------------------------------------------------------------

 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================

 

 


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