AMBER: problems with restart of smd simulation w/ jar=1 & nmr=1

From: Wei Chen <>
Date: Thu, 29 Nov 2007 12:15:51 -0500


As I posted earlier, I ran a smd simulation with GBSA on (jar=1, nmr=1,
igb=2, gbsa=1). When I restarted the smd simulation, I observed the sudden
drop of force. So I did some tests with different parameters. Now I have
some questions.

1. When I set nstlim=0, the output coordinates and velocities are different
from input ones. The output of nstlim=0 is the same as nstlim=1. Does the
program still go forward one step even with nstlim=0?

2. When I set nrespa=1 or 2 (nstlim=0 in both cases), the outputs are
different. Why are they different? Is something not calculated when
nrespa=1? I found GB cost time is less when nrespa=1.

3. When I turn smd on or off (on: jar=1, nmr=1; off: jar=0, nmr=0), the
outputs are the same. Since this is a restart from the middle of a smd
simulation, the loading force should not be zero at step 0. So I guess the
force is not on at step 0, but is switched on at step 1. Therefore it
generates a discontinuity, which causes the sudden drop of force I

My control file is as follows:

    ntc=2, ntf=2,
    cut=16.0, ntb=0, ntr=1,
    nstlim=0, dt=0.002, nrespa=2,
    ntt=3, gamma_ln=1.0, temp0=300.0,
    igb=2, saltcon=0.15, gbsa=1, surften=0.005,
    intdiel=1.0, extdiel=80.0, rgbmax=25.0,
    ntx=5, irest=1, ntpr=1, ntwx=1, ntwr=1,
    ntwv=1, nmropt=1,
 &wt type='DUMPFREQ', istep1=1, /
 &wt type='END', /

Thank you for any replies!

Wei Chen

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Received on Sun Dec 02 2007 - 06:07:22 PST
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