<div style="line-height:1.7;color:#000000;font-size:14px;font-family:arial">Thank you very much for your reply, Mark<br><br>It is the topology problem. It seems I did it in a wrong way. Now the topology goes like this: <br> <span style="FONT-SIZE: 18px"> <span style="FONT-SIZE: 13px"> [ molecules ]<br> ; Compound #mols<br> Protein_chain_A 1 <br> Protein_chain_A2 1<br> POPC 256</span></span><br>This problem solved.<br><br>But then comes a new one. When I did the g_membed, the system blowed up after one iteration!<br>I think I really shouldn't ignore the warning from the grompp. However, as an inexper
ienced user, I don't know how to improve the mdp file. Can you give me any hint?<br>The mdp file for the g_membed is like this:<br><blockquote><span style="font-size: 13px;">cpp = /lib/cpp</span><br><span style="font-size: 13px;">; Run parameters</span><br><span style="font-size: 13px;">integrator = md </span><br><span style="font-size: 13px;">nsteps = 1000 </span><br><span style="font-size: 13px;">dt = 0.002 </span><br><span style="font-size: 13px;">; Output control</span><br><span style="font-size: 13px;">nstxout = 10&n
bsp; </span><br><span style="font-size: 13px;">nstvout = 10 </span><br><span style="font-size: 13px;">nstenergy = 10 </span><br><span style="font-size: 13px;">nstlog = 10 </span><br><span style="font-size: 13px;">; Bond parameters</span><br><span style="font-size: 13px;">continuation = no </span><br><span style="font-size: 13px;">constraint_algorithm = lincs </span><br><span style="font-size: 13px;">constraints = all-bonds </span><br><span style="font-size: 13px;">lincs_iter
= 1 </span><br><span style="font-size: 13px;">lincs_order = 4 </span><br><span style="font-size: 13px;">; Neighborsearching</span><br><span style="font-size: 13px;">ns_type = grid </span><br><span style="font-size: 13px;">nstlist = 1 </span><br><span style="font-size: 13px;">rlist = 1.4 </span><br><span style="font-size: 13px;">rcoulomb = 1.4 </span><br><span style="font-size: 13px;">rvdw &nb
sp; = 1.4 </span><br><span style="font-size: 13px;">; Electrostatics</span><br><span style="font-size: 13px;">coulombtype = PME </span><br><span style="font-size: 13px;">pme_order = 4 </span><br><span style="font-size: 13px;">fourierspacing = 0.16 </span><br><span style="font-size: 13px;">; Temperature coupling is on</span><br><span style="font-size: 13px;">tcoupl = V-rescale </span><br><span style="font-size: 13px;">tc-grps = Protein Non-Protein </span><br><span style="font-size: 13px;">tau_t = 0.1 0.1 &
nbsp; </span><br><span style="font-size: 13px;">ref_t = 300 300 </span><br><span style="font-size: 13px;">; Pressure coupling is on</span><br><span style="font-size: 13px;">Pcoupl = Berendsen</span><br><span style="font-size: 13px;">pcoupltype = semiisotropic</span><br><span style="font-size: 13px;">tau_p = 1.0</span><br><span style="font-size: 13px;">compressibility = 4.5e-5 4.5e-5</span><br><span style="font-size: 13px;">ref_p  
; = 1.0 1.0</span><br><span style="font-size: 13px;">; Velocity generation</span><br><span style="font-size: 13px;">gen_vel = yes</span><br><span style="font-size: 13px;">gen_temp = 300</span><br><span style="font-size: 13px;">gen_seed = 173529</span><br><span style="font-size: 13px;">; Energy monitoring</span><br><span style="font-size: 13px;">energygrps = Protein</span><br><span style="font-size: 13px;">; Non-equilibrium MD</span><br><span style="font-size: 13px;">freezegrps = Protein</span><br><span style="font-size: 13px;">freezedim &nb
sp; = Y Y Y</span><br><span style="font-size: 13px;">; Energy group exclusions</span><br><span style="font-size: 13px;">energygrp_excl = Protein Protein</span><br></blockquote><br><div></div><div id="divNeteaseMailCard"></div>Thanks a lot!<br>Linda<br><br><br><br></div><br><br><span title="neteasefooter"><span id="netease_mail_footer"></span></span>