AMBER Archive (2009)

Subject: [AMBER] Thermodynamic Integration at higher values of clambda using AMBER 9

From: PRADEEP VENKATARAMAN (pvtulane_at_gmail.com)
Date: Thu Mar 12 2009 - 16:56:59 CDT

Hi,

I am using Amber 9 thermodynamic integration utility to calculate
disappearance of all atom methane from my system.

I am running NPT for simulation for 2 ns for obtaining the equilibrium
structure at every clambda followed by NVE simulations for 5 ns.

The system works fine for clambda 0.00 to 0.80 (I am using a different
technique of numerical integration instead of using the Gaussian quadrature
suggested in the manual).

When I run the disappearing free energy calculation at clambda 0.90 and
higher I get the following error during NVE simulation.

check COM velocity, temp: 0.000000 0.00(Removed)
check COM velocity, temp: 0.000000 0.00(Removed)
check COM velocity, temp: 0.000000 0.00(Removed)
check COM velocity, temp: 0.000000 0.00(Removed)
vlimit exceeded for step 486032; vmax = 73.1079
vlimit exceeded for step 486033; vmax = 20.0107
vlimit exceeded for step 486034; vmax = 21.2457
vlimit exceeded for step 486036; vmax = 28.6820

     Coordinate resetting (SHAKE) cannot be accomplished,
     deviation is too large
     NITER, NIT, LL, I and J are : 0 0 2086 384 413

     Note: This is usually a symptom of some deeper
     problem with the energetics of the system.

My input file for NPT simulation is as below

 &cntrl
   imin=0, ntx=5, irest=1, ntp=1, ntb=2,
   ntf=2, ntc=2, ntt=2, ntrx=1, ntr=0,
   temp0= 240., tempi= 240., pres0= 120.,
   taup=2.0, tautp=1.0, cut=8.0, ig=342786,
   dt=0.002, comp=44.6, icfe=1, clambda=0.90,
   nstlim=1000000, ntave=50000, ntpr=50000,
   ntwr=1000, ntwx=0, ntwe=50000, klambda=6,
 /

 and input file for NVE simulation is as below

 &cntrl
   imin=0, ntx=7, irest=1, ntp=0, ntb=1,
   ntf=2, ntc=2, ntt=0, ntrx=1, ntr=0,
   temp0= 240., tempi= 240., pres0= 120.,
   taup=2.0, tautp=1.0, cut=8.0, ig=342786,
   dt=0.002, comp=44.6, icfe=1, clambda=0.90,
   nstlim=2500000, ntave=250000, ntpr=250000,
   ntwr=1000, ntwx=0, ntwe=250000, klambda=6,
 /

Please help me understand why this is happening. If you want to take a look
at prmtop file, I would be glad to send it to you by e-mail.

Thanks,

Pradeep
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