AMBER: density problem

From: cristian obiol <>
Date: Tue, 31 May 2005 11:17:46 +0200

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 :

     imin=0, irest=0, ntx=1, ntx=7,
     ntc=2,ntf=2, tol=0.000001,
     cut = 9.0,
     ntt=1, tautp=1.0, taup=0.2, tempi=300.0, temp0=300.0,
     ntwv=1000, ntwe=1000, ntwx=1000,ntwr=1000,
 Restrictions to solute
RES 1 102

Thanks in advance,

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

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Received on Tue May 31 2005 - 10:53:00 PDT
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