[AMBER] md simulation-cap

From: Rilei Yu <yulaomao1983.yahoo.com.cn>
Date: Sun, 2 May 2010 20:40:16 +0800 (CST)

Dear AMBER users,

Recently, I tried to using solvatecap to simulate my system for faster speed. Unfortunately, sometime the ligands change drastically, even the ligand goes out the binding site in some simulation.

I try to solve this problem using all kinds of ways:
extending the cap radius;
using smaller steps(0.001);
adding some restraint;
slowly increasing T;
Unfortunately, the system is still not very stable as I expected. Here, I give the simulation file as follows and really hope anyone can give me some suggestions:
&cntrl
  ntx=5,
  irest=1,
  imin=0,
  ntpr=1000,
  ntwx=1000,
  ntwr=5000,
  nstlim=250000,
  dt=0.001,
  ntt=3,
  gamma_ln = 1.0,   
  temp0=300,
  tempi=300,
  tautp=1,
  igb=0,
  ntb=0,
  ntf=2,                                                                      
  ntc=2, 
  cut=15, 
  ntr=1,
  fcap=2.5,
  ivcap=0,
  tol=0.000001,
  ntr=1, restraint_wt=5.0, restraintmask=':1-92, 95-144, 153-185, 200-243, 251-266, 273-288, 292-320, 324-326, 332-372, 375-377, 382-419',
  &end
I am really appreciated for your help!

Rilei Yu
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Received on Sun May 02 2010 - 06:00:16 PDT
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