Dear Amber User
I am trying to perform Temperature REMD simulation of proteins in water. My
temp range from 280-600K, I started with minimized and NPT equilibrated
(for 2ns at 300K) system as starting structure. Then this system slowly
heating to the assign desired temp and then further these system are
equilibration (NPT ) at that temperature. All the trajectory are stable
below 500 K and above 500K temperature system start blowing, box volume
increasing continuously resulted into continuously decreasing in density.
At temperature 590 to 600K, system terminated with SANDER BOMB error.
My common input file for simulation is given here.
1 atm, NPT,
&cntrl
imin = 0, ntx = 5, irest = 1,
nstlim = 2000000, dt =0.001, cut=10.0,
ntpr = 100, ntwx = 100, ioutfm = 1,
ntc = 2, ntf = 2, ntxo = 1, iwrap=1,
ntb = 2, tautp =2.0, ig = RANDOM_NUMBER,
tempi = XXXXX, temp0 = XXXXX, ntt =3, gamma_ln = 1,
ntp = 1, taup = 2.0, pres0 =1.0, nmropt=1
&end
&ewald
EW_TYPE=1
&end
/
&wt TYPE='END'
/
DISANG=trpcage.CHIR.dat
1) Is there any unusual parameter in my input file.
2) How to equilibrate my system above 500 K (maintained density before REMD)
Thank you in advance
Regards
Rahman
'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
*M*d* H*omaidur* R**ahman *( Research Scholar )
Lab No. 510, Computational Biophysics Lab.
Department of Biotechnology
Indian Institute of Technology-Madras
Chennai-600 036, India
*Mobile No = +91- 7845991785*
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Received on Sun Apr 09 2017 - 09:00:02 PDT
