Rilei Yu
--- 10年5月2日，周日, Rilei Yu <yulaomao1983.yahoo.com.cn> 写道：
发件人: Rilei Yu <yulaomao1983.yahoo.com.cn>
主题: [AMBER] md simulation-cap
收件人: amber.ambermd.org
日期: 2010年5月2日,周日,下午8:40
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 - 17:00:03 PDT
