[AMBER] Error when running MD

From: maya nair <mayasnair1.gmail.com>
Date: Fri, 13 Dec 2019 23:21:34 +0530

Dear Amber users,
I am trying to do a nmr refined MD simulation. Minimization was done for
the system without any error. When doing MD with the protocol
simulated annealing protocol, 20 ps


    nstlim=20000, nscm=1000, pencut=-0.001, nmropt=1,
    ntpr=200, ntt=1, ntwx=200,
    cut=15.0, ntb=0, vlimit=10,

#Simple simulated annealing algorithm:


#from steps 0 to 5000: heat the system to 600K
#from steps 5001-18000: re-cool to low temperatures with long tautp
#from steps 18001-20000: final cooling with short tautp

 &wt type='TEMP0', istep1=0,istep2=5000,value1=600.,
            value2=600., /
 &wt type='TEMP0', istep1=5001, istep2=18000, value1=600.0,
            value2=100.0, /
 &wt type='TEMP0', istep1=18001, istep2=20000, value1=0.0,
            value2=0.0, /

 &wt type='TAUTP', istep1=0,istep2=5000,value1=0.4,
            value2=0.4, /
 &wt type='TAUTP', istep1=5001,istep2=18000,value1=4.0,
            value2=4.0, /
 &wt type='TAUTP', istep1=18001,istep2=19000,value1=1.0,
            value2=1.0, /
 &wt type='TAUTP', istep1=19001,istep2=20000,value1=0.1,
            value2=0.05, /

 &wt type='REST', istep1=0,istep2=3000,value1=0.1,

            value2=1.0, /
 &wt type='REST', istep1=3001,istep2=20000,value1=1.0,

            value2=1.0, /

 &wt type='END' /

I got the following message after runnung MD for only 1.6ps
Frac coord min, max: 0.15981055968035968 1.0005435873364954
 The system has extended beyond
     the extent of the virtual box.
 Restarting sander will recalculate
    a new virtual box with 30 Angstroms
    extra on each side, if there is a
    restart file for this configuration.
 SANDER BOMB in subroutine Routine: map_coords (ew_force.f)
 Atom out of bounds. If a restart has been written,
 restarting should resolve the error.
There is no restart file generated . How will I solve this error.
I put nscm=1000 after going through some former messages, but getting the
same message. If anybody knows , please help out me.

Thank you,

Maya S Nair
Assistant Professor
Department of Biotechnology
IIT Roorkee
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Received on Fri Dec 13 2019 - 10:00:02 PST
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