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Thanks, David. The energies after SD-EM seem ok.<br>
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What do I do with the PR-MD and the LINCS warning? Please, see the GPCR_popc_pr.mdp
below.<br>
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<blockquote type="cite" cite="mid:1068583892.1812.4.camel@h28n2fls34o1123.telia.com">
<pre wrap="">On Tue, 2003-11-11 at 21:07, Martina Bertsch, PhD wrote:<br></pre>
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<pre wrap="">Dear colleagues,<br><br><!---->I use the final structure from my EM run as an input for the PR-MD. <br>My GPCR_popc_pr.mdp is attached below.<br><br>When I try running mdrun, I get a LINCS warning:<br><br> "Relative constraint deviation after LINCS"<br><br>and the simulation stops at step 0.<br><br>How can I modify my *pr.mdp to remedy this?<br><br>Your advice is appreciated.<br><br>Best regards,<br><br>Martina Bertsch, Ph.D.<br>Northwestern University<br>Feinberg School of Medicine<br>Molecular Pharmacology and Biological Chemistry<br>303 East Chicago Avenue<br>Chicago, IL 60611<br><br><br>______________________________________________________________________<br><br>title = GPCR in POPC PR-MD<br>cpp = /lib/cpp<br>define = -DFLEX_SPC<br>define = -DPOSRES<br>constraints = all-bonds<br>constraint_algorithm = lincs<br>integrator = md<br>dt = 0.001 ; ps !<br>ns
teps = 5000000 ; total 5 ns<br>;nstcomm = 1<br>nstxout = 5000<br>nstvout = 5000<br>nstfout = 5000<br>nstlog = 5000<br>nstenergy = 5000<br>nstxtcout = 5000<br>nstlist = 10<br>ns_type = grid<br>rlist = 1.0<br>coulombtype = PME<br>rcoulomb = 1.0<br>rvdw = 1.2<br>pbc = xyz<br>comm_mode = linear<br>nstcomm = 1<br>fourierspacing = 0.15<br>pme_order = 4<br>optimize_fft = yes<br>comm_grps = popc sol<br>; Berendsen temperature coupling is on in two groups<br>Tcoupl = berendsen<br>tau_t = 0.1 0.1 0.1<br>tc-grps = protein popc sol<br>ref_t = 300 300 300<br>; Energy monitoring<br>energygrps = protein popc sol<br>; Pressure coupling is on<br
>Pcoupl = berendsen<br>pcoupltype = anisotropic<br>tau_p = 5 5 5 0 0 0<br>compressibility = 4.5e-5 4.5e-5 4.5e-5 0 0 0<br>ref_p = 1.0 1.0 1.0 0 0 0<br>; Generate velocites is on at 300 K.<br>gen_vel = yes<br>gen_temp = 300.0<br>gen_seed = 280572<br></pre>
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