[AMBER] Nothing returned in aMD simulation of membrane protein

From: Meng Wu <wumeng.shanghaitech.edu.cn>
Date: Tue, 26 Feb 2019 05:42:52 +0000

Dear Amber experts,

I've tried to apply accelerated MD for the simulation of membrane protein following the tutorial "Advanced Tutorial 22 Introduction" on AMBER16. However, the job was terminated very soon and nothing returned in out file. Here is my in file:

aMD 100ns LIPID 303K
   imin=0, ntx=5, irest=1,
   ntc=2, ntf=2, tol=0.0000001,ntwv=-1,
   nstlim=50000000, ntt=3, gamma_ln=1.0,
   ntpr=5000, ntwr=500000, ntwx=5000,
   dt=0.002, ig=-1,
   ntb=2, cut=10.0, ioutfm=1, ntxo=2,
   ntp=3, csurften=3, gamma_ten=0.0, ninterface=2,

When calculating E(dih) and Alpha(dih), both protein and membrane were accounted as solute in aMD parameters settings.

Out file has been attached, no error file returned. And if I remove aMD parameters "iamd=3,ethreshd=11799,alphad=481.6,ethreshp=-86323.08,alphap=8773.92,", it could run normally.

I would appreciate if someone can tell me what's wrong with my aMD simulation.

Thank you,

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Received on Mon Feb 25 2019 - 22:00:03 PST
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