<br /><br /><span>On 04/08/11, <b class="name">xiaowu759 </b> <xiaowu759@qq.com> wrote:</span><blockquote cite="mid:tencent_704FC6D7086CB92D036ABB80@qq.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html"><div>Dear gmxers,</div>
<div>I try to perform NPT MD to obtain the density of system. But the value of density does not stablize even after over 40 ns. The content of mdp file can be seen below. How to deal with it? Please give me some hints. Thanks a lot for any replies.</div></div></blockquote><br />We have no idea whether your judgement that density is not stabilized after 40ns is sound, because you provided no data. Your temperature coupling is to group "Other", which may or may not be reasonable. Your integration time step is possibly too large for a simulation using no bond constraints. Your initial density could be so far from correct that reaching equilibrium is infeasible. You'll need to provide a lot more information to get useful help.<br /><br />Mark<br /><br /><blockquote cite="mid:tencent_704FC6D7086CB92D036ABB80@qq.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html"><div ><br/></div>
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<div>.mdp file: </div>
<div>title = </div>
<div>cpp = /lib/cpp<br />include = -I../top<br />define = ;{-DFLEXIBLE,-DPOSRES} <br />integrator = md<br />dt = 0.001<br />comm_mode = Linear ;{Linear,Angular,No}<br />nstcomm = 10<br />nstcalcenergy = 1<br />nsttcouple = 1<br />nstpcouple = 1<br />comm_grps = <br />nsteps = 25000000<br />nstxout = 1000<br />nstvout = 1000<br />nstlog = 1000<br />nstenergy = 1000<br />nstxtcout = 1000<br />nstlist = 10<br />ns_type = grid ;{simple,grid}<br />rlist = 1.0<br />coulombtype = pme<br />fourierspacing = 0.12 ; [0.12 nm]<br />optimize_fft = yes ;{no,yes}<br />rcoulomb = 1.0<br />rvdw = 1.0<br />DispCorr = EnerPres ;{no,EnerPres,Ener}<br />pbc = xyz ; Periodic Boundary Conditions {xyz,no,xy}<br />tcoupl = berendsen ;no,berendsen,nose-hoover,v-rescale<br />tc-grps = Other <br />tau_t = 0.1 <br />ref_t = 600 <br />Pcoupl = berendsen ;{no,berendsen,Parrinello-Rahman}<br />Pcoupltype = isotropic ;{isotropic,semiisotropic;anisotropic;surface-tension}<br />tau_p = 0.1<br />compressibility = 4.5e-5<br />ref_p = 1.0 ;the unit is bar(1 bar =10^5 Pa)<br />gen_vel = no <br />gen_temp = 600<br />gen_seed = 173529<br />constraints = none ;{none,hbonds,all-bonds,h-angles,all-angles}<br />constraint_algorithm = LINCS ;{LINCS,SHAKE}<br />periodic_molecules = no ;{no,yes}</div>
<div>annealing = no ;{no,single,periodic}<br />annealing_npoints = 11<br />annealing_time = 0 100 200 300 400 500 600 700 800 900 1000<br />annealing_temp = 600 580 560 540 520 500 520 540 560 580 600<br /></div>
<div>Best regards,</div>
<div>Dr. Chaofu Wu</div>
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