Re: [AMBER] Error when running MD

From: Bill Ross <>
Date: Fri, 13 Dec 2019 11:02:13 -0800

Looks like your initial temp is 600K. Very hard to go 0..600K w/o warming steps, unless the system is rather simple.BillAI:
-------- Original message --------From: maya nair <> Date: 12/13/19 9:51 AM (GMT-08:00) To: AMBER Mailing List <> Subject: [AMBER] Error when running MD Dear Amber users,I am trying to do a nmr refined MD simulation. Minimization was done forthe system without any error. When doing MD with the protocolsimulated annealing protocol, 20 ps &cntrl    nstlim=20000, nscm=1000, pencut=-0.001, nmropt=1,    ntpr=200, ntt=1, ntwx=200,    cut=15.0, ntb=0, vlimit=10, / &ewald    eedmeth=5, /##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'  /LISTOUT=POUTDISANG=newRSTAI got the following message after runnung MD for only 1.6psFrac 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 thesame message. If anybody knows , please help out me.Thank  you,Maya-- Maya S NairAssistant ProfessorDepartment of BiotechnologyIIT RoorkeeIndia_______________________________________________AMBER mailing listAMBER.ambermd.org
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Received on Fri Dec 13 2019 - 11:30:01 PST
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