AMBER Archive (2005)

Subject: AMBER: density problem

From: cristian obiol (c.obiol_at_qf.ub.es)
Date: Tue May 31 2005 - 04:17:46 CDT


Dear Amber users,

I'm running sander 7 in linux platform,
My problem deals with the P constant step in which the density normally
achieve a value near 1.0. I nottice that my density is about 0.7 with very
slow increments. Seeing my water box, it has 4 holes in the edges that don't
disappear. I try to set taup=0.1 but even in this manner it does not
function. These strange holes were created in the previous heat up step.
Here is my input :

 &cntrl
     imin=0, irest=0, ntx=1, ntx=7,
     ntpr=1000,
     ntc=2,ntf=2, tol=0.000001,
     cut = 9.0,
     scee=1.2,
     ntb=2,
     ntp=1,
     nstlim=60000,
     ntt=1, tautp=1.0, taup=0.2, tempi=300.0, temp0=300.0,
     ntwv=1000, ntwe=1000, ntwx=1000,ntwr=1000,
     ntr=1,ibelly=0,iwrap=1,
 &end
 Restrictions to solute
 500.0
RES 1 102
END
END

Thanks in advance,

Cristian Obiol
Biological Systems Modelling
and Drug Design Research Group
University of Barcelona

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