<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Hello All,<br><br>With regard to my previous post <br>http://www.mail-archive.com/gmx-users@gromacs.org/msg30557.html<br>I have done postion restrained energy minimisation using POSRES.itp file obtained from pdb2gmx. so that there should not be any large change in the strucutre of the protein.<br>And after that I did equilbration using following mdp file<br><br>title = protein<br>cpp = /usr/bin/cpp<br>define = -DPOSRES<br>constraints = all-bonds<br>integrator =
md<br>dt = 0.002 ; ps !<br>nsteps = 10000 ; total 20.0 ps.<br>nstcomm = 1<br>nstxout = 250 ; collect data every 0.5 ps<br>nstvout = 1000<br>nstfout = 0<br>nstlog = 10<br>nstenergy = 10<br>nstlist =
5<br>ns_type = grid<br>rlist = 0.9<br>coulombtype = PME<br>rcoulomb = 0.9<br>rvdw = 1.4<br>fourierspacing = 0.12<br>fourier_nx = 0<br>fourier_ny = 0<br>fourier_nz = 0<br>pme_order = 4<br>ewald_rtol = 1e-5<br>optimize_fft = yes<br>; Berendsen temperature
coupling is on in two groups<br>Tcoupl = V-rescale<br>tc-grps = Protein Non-Protein<br>tau_t = 0.1 0.1 <br>ref_t = 300 300 <br>; Pressure coupling is on<br>Pcoupl = berendsen<br>tau_p = 0.5<br>compressibility = 4.5e-5<br>ref_p = 1.0<br>; Generate velocites is on at 300
K.<br>gen_vel = yes<br>gen_temp = 300.0<br>gen_seed = 173529<br><br>After this, I put the molecule for simulation using the following .mdp file<br><br>title = protein<br>cpp = /usr/bin/cpp<br>constraints = all-bonds<br>integrator = md<br>dt = 0.002 ; ps !<br>nsteps = 500000 ; total 1000 ps, 1
ns.<br>nstcomm = 1<br>nstxout = 500 ; collect data every 1 ps<br>nstvout = 0<br>nstfout = 0<br>nstlist = 5<br>ns_type = grid<br>rlist = 0.9<br>coulombtype = PME<br>rcoulomb = 0.9<br>rvdw =
1.4<br>fourierspacing = 0.12<br>fourier_nx = 0<br>fourier_ny = 0<br>fourier_nz = 0<br>pme_order = 4<br>ewald_rtol = 1e-5<br>optimize_fft = yes<br>; Berendsen temperature coupling is on in two groups<br>Tcoupl = V-rescale<br>tc-grps = Protein Non-Protein<br>tau_t = 0.1 0.1
<br>ref_t = 300 30<br>; Pressure coupling is on<br>Pcoupl = berendsen<br>tau_p = 0.5<br>compressibility = 4.5e-5<br>ref_p = 1.0<br>; Generate velocites is on at 300 K.<br>gen_vel = yes<br>gen_temp = 300.0<br>gen_seed = 173529<br><br>but simulation has crashed showing the error too many<span style="font-weight: bold;"> Too many LINCS warnings (1000)<br></span>I checked previous
posts, it is given that it may be due to incomplete equilibration or putting so many constraints.<br>So can you please help me in correcting it.<br>Thanks and regards.<br><span style="font-weight: bold;"></span><br><div>--<br>Sonali Dhindwal</div></td></tr></table><br>