AMBER Archive (2002)

Subject: Running TIP5P with PBC

From: Sarah Tschampel (tschampe_at_sunchem.chem.uga.edu)
Date: Wed Jul 03 2002 - 14:47:41 CDT

Hi,

I am trying to use amber7 to run a constant pressure simulation with TIP5P
as the solvent. I did this successfully for TIP4P solvating with the
preequilibrated box of TIP4P. Since there is not an equivalent for TIP5P
I am trying to obtain such a box. I have tried many things, heating over
longer times (from 50-1000ps), trying NTT=1 and 4, as well as removing
translational motion more that every 1000 steps. Also, I have tried to
run a constant volume simulation first, but when I try to run constant
pressure from the output it still fails.

Here is an example of one input file I have tried:

heating tip5p box of water
 &cntrl
 IREST=0, IMIN=0, NMROPT=1, NTPR=5000,
 NTX=1, IG=71277, TEMPI=5.0, HEAT=5.0,
 NTB=2, NTC=2, TOL=0.0005, NTF=2, NSNB=25,
 NTT=4, TEMP0=300.0, DTEMP=5.0, TAUTP=0.25,
 NTP=2, PRES0=1.0, COMP=44.6,
 NSTLIM=300000, 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=500, NSCM = 100,
 &end
 &wt
   TYPE='TEMP0',ISTEP1=1,ISTEP2=250000,VALUE1=5.0,VALUE2=300.0,
 &end
 &wt
   TYPE='TEMP0',ISTEP1=250001,ISTEP2=300000,VALUE1=300.0,VALUE2=300.0,
 &end
 &wt TYPE='END'
 &end END

Any help would be greatly appreciated,

Thanks,
Sarah