AMBER Archive (2008)

Subject: AMBER: question about pression

From: Yunierkis Perez Castillo (Yunierkis_at_uclv.edu.cu)
Date: Mon Oct 13 2008 - 09:45:38 CDT

Hi all.
I have prepared a MD simulation of a protein with solvent and counterions in an octahedron box using the same parameters set given in the amber manual for a "plain MD simulation". Here is my input file:

 &cntrl
  nstlim=5000000, dt=0.002, ntx=5, irest=1, ntpr=500, ntwr=5000,
  ntwx=5000,

  ntt=3, gamma_ln = 5.0, tempi = 300.0, temp0=300.0,

  ntb=2, ntp=1, taup=2.0

  ntc=2, ntf=2,

  nrespa=1,
/

By looking the output file I can see that the pressure have great fluctuation, while T fluctuations , nevertheless the reported average pressure at the end of the simulation is 1.0.
Shouldn't pressure fluctuations be smaller??
I have no much experience in MD simulations, so, sorry if this is a RTFM question.
Here is part of the output file (only the line regarding pressure information

 NSTEP = 500 TIME(PS) = 121.000 TEMP(K) = 300.88 PRESS = -129.1
 NSTEP = 1000 TIME(PS) = 122.000 TEMP(K) = 300.23 PRESS = -130.1
 NSTEP = 1500 TIME(PS) = 123.000 TEMP(K) = 299.49 PRESS = 16.1
 NSTEP = 2000 TIME(PS) = 124.000 TEMP(K) = 299.41 PRESS = -124.0
 NSTEP = 2500 TIME(PS) = 125.000 TEMP(K) = 300.10 PRESS = -24.4
 NSTEP = 3000 TIME(PS) = 126.000 TEMP(K) = 300.66 PRESS = 40.4
 NSTEP = 3500 TIME(PS) = 127.000 TEMP(K) = 299.67 PRESS = -30.6
...............................................

Thanks in advance for any answer.
yunierkis

Servicio de Correos de la Universidad Central "Marta Abreu" de Las Villas. http://www.uclv.edu.cu
-VI Conferencia Internacional de Ciencias Empresariales, del 16 al 18 de octubre de 2008, Cayo Santa Mar?a, Cuba. http://economia-publica.uab.es/VIcubaCICE.doc
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