SITS production

#分子模拟最基本相关设置
mode = NVT

dt = 2e-3
step_limit = 10000000
write_information_interval = 500
write_restart_file_interval = 5000
molecule_map_output = 1

cutoff = 8

#热浴相关
target_temperature = 300.0 #模拟的目标平衡温度，单位为开
thermostat = langevin #可选热浴见下
langevin #居中图示的langevin算法
{
    seed = 1  #随机数种子，不填随机生成
    gamma = 10.0  #摩擦系数（碰撞频率），单位为ps^-1
    velocity_max = 20.0 #迭代时速度的最大值，单位为埃每皮秒
}

constrain_mode = SHAKE



        amber_rst7 = ala_1987.rst7        
        amber_parm7 = ala_1987.parm7
        mdout = mdout.txt   #记录能量轨迹的文件
        mdinfo = mdinfo.txt #记录参数相关的文件
        box = mdbox.txt       #记录盒子轨迹的文件
        crd = mdcrd.dat        #记录坐标轨迹的文件
        rst = restart            #记录重启坐标和速度的文件

#SITS相关

SITS_k_numbers = 40
SITS_T_low = 250
SITS_T_high = 600
SITS_protein_numbers = 22
SITS_nk_rest = 1
SITS_nk_in_file = SITS_nk_rest_ala.txt
SITS_nk_fix = 1
SITS_pe_b = -20


end_pause = 0
