AMBER Archive (2007)

Subject: AMBER: TIP5P water Simulation

From: Biman Jana (bjana_at_sscu.iisc.ernet.in)
Date: Wed Nov 07 2007 - 11:12:42 CST

  I was trying to do the bulk water simulation with tip5p model. I
have first equilibrated the system at constant volume simulation to 300K.
Then i was running NPT simulation, it is showing the error after some steps
" vlimit exceeded" and after that all the quantity is becomung NAN and
simulation is getting stuck. I have attached the simulation controll
parameter file (AMBER7) used in the simulation. Can you please let me know
where I am going wrong. I have also simulate the DNA (may be 12 base pairs
long) with TIP5P water also. I have the simulation controll file for TIP3P
water. But that is not working for TIP5P case, giving the error mentioned
above. I will be very much grateful to you, if you suggest me something so
that i can come out of the problem. Thanking you.

Biman Jana

Here is the input file

&cntrl
   IREST=1, IMIN=0, NMROPT=0, NTPR=100,
   NTX=5, IG=71277, TEMPI=300, HEAT=5.0,
   NTB=2, NTC=2, TOL=0.0005, NTF=2, NSNB=25,
   NTT=1, TEMP0=300.0, DTEMP=5.0, TAUTP=1.0,
   NTP=1, PRES0=1.0, COMP=44.6,TAUP=0.5
   NSTLIM=100000, T=0.0, DT=0.002,
   CUT=8.0, SCNB=2.0, SCEE=1.2, DIELC=1.0,
   DX0=0.01, DXM=0.5,
   IBELLY=0, NTWX=10, NSCM = 1000,NTWR=500
   &end
&ewald
   SKINNB=1.5,
  & end
  & wt
     TYPE='TEMP0',ISTEP1=1,ISTEP2=100000,VALUE1=300.0,VALUE2=300.0,
  & end
  & wt TYPE='END'
  & end END 

-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu

-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu